Long-range interactions between the Fe protein binding sites of the MoFe protein of nitrogenase

We report the properties and reactivity of the catalytically active heterologous nitrogenase formed between the Fe protein from Clostridium pasteurianum (Cp2) and the MoFe protein from Klebsiella pneumoniae (Kp1). Under turnover conditions, in the presence of MgATP, a stable 2:1 (Cp2)2Kp1 electron transfer complex is formed, in which the [4Fe-4S]+ centre of Cp2 is protected from chelation by alpha,alpha'-bipyridyl. However, the two Fe protein-binding sites on Kp1 are not equivalent, since a 1:1 Cp2.Kp1 complex was isolated by gel filtration. The non-equivalence of the Fe protein binding sites was also indicated by the inhibition pattern of Klebsiella nitrogenase by Cp2. The EPR spectrum of the isolated 1:1 Cp2.Kp1 complex showed an S=1/2 signal characteristic of dithionite-reduced Cp2 and signals with g values of 4.27, 3.73, 2.01 and 4.32, 3.63, 2.00 characteristic of the high- and low-pH forms of the FeMoco centre of Kp1, respectively. The unoccupied binding site of Kp1 of the isolated 1:1 Cp2Kp1 complex was shown to be catalytically fully functional in combination with Kp2. In contrast to homologous nitrogenases, which require MgATP for detectable rates of electron transfer from the Fe protein, stopped-flow kinetic studies revealed that electron transfer from Cp2 to Kp1 occurred in the absence of MgATP with a rate constant of 0.065 s(-1). Subsequently, a slower transient decrease and restoration of absorption in the electronic spectrum in the 500-700 nm region was observed. These changes corresponded with those in the intensity of the S=3/2 EPR signal of the FeMoco centres of Kp1 and were consistent with the transient reduction of the FeMoco centre of Kp1 to an EPR-silent form, followed by restoration of the signal at longer reaction times. These changes were not associated with catalysis since no evolution of H2 was detectable.     

Conformational Properties of Seven Toac-Labeled Angiotensin I Analogues Correlate with Their Muscle Contraction Activity and Their Ability to Act as ACE Substrates

Conformational properties of the angiotensin II precursor, angiotensin I (AngI) and analogues containing the paramagnetic amino acid TOAC (2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) at positions 0, 1, 3, 5, 8, 9, and 10, were examined by EPR, CD, and fluorescence. The conformational data were correlated to their activity in muscle contraction experiments and to their properties as substrates of the angiotensin I-converting enzyme (ACE). Biological activity studies indicated that TOAC⁰-AngI and TOAC¹-AngI maintained partial potency in guinea pig ileum and rat uterus. Kinetic parameters revealed that only derivatives labeled closer to the N-terminus (positions 0, 1, 3, and 5) were hydrolyzed by ACE, indicating that peptides bearing the TOAC moiety far from the ACE cleavage site (Phe⁸-His⁹ peptide bond) were susceptible to hydrolysis, albeit less effectively than the parent compound. CD spectra indicated that AngI exhibited a flexible structure resulting from equilibrium between different conformers. While the conformation of N-terminally-labeled derivatives was similar to that of the native peptide, a greater propensity to acquire folded structures was observed for internally-labeled, as well as C-terminally labeled, analogues. These structures were stabilized in secondary structure-inducing agent, TFE. Different analogues gave rise to different β-turns. EPR spectra in aqueous solution also distinguished between N-terminally, internally-, and C-terminally labeled peptides, yielding narrower lines, indicative of greater mobility for the former. Interestingly, the spectra of peptides labeled at, or close, to the C-terminus, showed that the motion in this part of the peptides was intermediate between that of N-terminally and internally-labeled peptides, in agreement with the suggestion of turn formation provided by the CD spectra. Quenching of the Tyr⁴ fluorescence by the differently positioned TOAC residues corroborated the data obtained by the other spectroscopic techniques. Lastly, we demonstrated the feasibility of monitoring the progress of ACE-catalyzed hydrolysis of TOAC-labeled peptides by following time-dependent changes in their EPR spectra.     

Contribution of hydrogen bonds to protein stability

Our goal was to gain a better understanding of the contribution of the burial of polar groups and their hydrogen bonds to the conformational stability of proteins. We measured the change in stability, Δ(ΔG), for a series of hydrogen bonding mutants in four proteins: villin headpiece subdomain (VHP) containing 36 residues, a surface protein from Borrelia burgdorferi (VlsE) containing 341 residues, and two proteins previously studied in our laboratory, ribonucleases Sa (RNase Sa) and T1 (RNase T1). Crystal structures were determined for three of the hydrogen bonding mutants of RNase Sa: S24A, Y51F, and T95A. The structures are very similar to wild type RNase Sa and the hydrogen bonding partners form intermolecular hydrogen bonds to water in all three mutants. We compare our results with previous studies of similar mutants in other proteins and reach the following conclusions. (1) Hydrogen bonds contribute favorably to protein stability. (2) The contribution of hydrogen bonds to protein stability is strongly context dependent. (3) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. (4) Polar group burial can make a favorable contribution to protein stability even if the polar groups are not hydrogen bonded. (5) The contribution of hydrogen bonds to protein stability is similar for VHP, a small protein, and VlsE, a large protein.     

The Performance of Mixture Models in Heterogeneous Closed Population Capture–Recapture

Summary .   Dorazio and Royle (2003, Biometrics 59, 351–364) investigated the behavior of three mixture models for closed population capture–recapture analysis in the presence of individual heterogeneity of capture probability. Their simulations were from the beta-binomial distribution, with analyses from the beta-binomial, the logit-normal, and the finite mixture (latent class) models. In this response, simulations from many different distributions give a broader picture of the relative value of the beta-binomial and the finite mixture models, and provide some preliminary insights into the situations in which these models are useful.     

Dnmt1 deficiency leads to enhanced microsatellite instability in mouse embryonic stem cells

DNA hypomethylation is frequently seen in cancer and imparts genomic instability in mouse models and some tissue culture systems. However, the effects of genomic DNA hypomethylation on mutation rates are still elusive. We have developed a model system to analyze the effects of DNA methyltransferase 1 (Dnmt1) deficiency on DNA mismatch repair (MMR) in mouse embryonic stem (ES) cells. We generated sibling ES cell clones with and without functional Dnmt1 expression, containing a stable reporter gene that allowed us to measure the slippage rate at a mononucleotide repeat. We found that Dnmt1 deficiency led to a 7-fold increase in the microsatellite slippage rate. Interestingly, the region flanking the mononucleotide repeat was unmethylated regardless of Dnmt1 status, suggesting that it is not the local levels of DNA methylation that direct the increase in microsatellite instability (MSI). The enhanced MSI was associated with higher levels of histone H3 acetylation and lower MeCP2 binding at regions near the assayed microsatellite, suggesting that Dnmt1 loss may decrease MMR efficiency by modifying chromatin structure.     

Substituted nitroguanidines provide cytokinin activity during in vitro cultivation of plant tissues

Synthetic nitroguanidine derivatives can be used as alternatives to the traditional adenine-containing cytokinins used in plant tissue culture. First, nitroguanidine derivatives (NG) mimicked the typical activity of two standard cytokinins, 6-benzylaminopurine (BAP) and 2-isopentenyladenine (2iP) in the soybean callus (Glycine max) growth bioassay. NGs caused unanticipated responses as well, as demonstrated in three lines of tobacco (Nicotiana tabacum), when the auxin concentration was reduced from the standard concentration of 2 ug/ml NAA, to much lower concentrations of 0.01 ug/ml NAA or 0.02 ug/ml IAA. At the low auxin concentrations, kinetin lost the ability to promote either growth or differentiation, while the NG cytokinins were fully able to promote both. NGs promoted growth and differentiation in the presence of 0.01 ug/ml NAA in a newly initiated, totipotent line of Coker 319 tobacco. NGs plus 0.02 ug/ml IAA also promoted callus growth in a cytokinin-habituated tobacco line, Havana 425-CH. Lastly, NGs stimulated the outgrowth of healthy callus from aged callus that had been allowed to deteriorate through lack of subculture. Upon transfer of aged NTP callus to fresh media with NGs and 0.02 ug/ml IAA, healthy cell clusters were rapidly produced. In all three cases cited above, kinetin was ineffective at the low auxin concentrations. The NGs are therefore cytokinins, with the additional possibility of reducing the level of auxin required for their activity to be expressed.Abbreviations BAP 6-benzylaminopurine or N⁶- benzyladenine - IAA indoleacetic acid - 2iP N⁶-(²- isopentenyl)adenine - NAA -naphthaleneacetic acid - NG nitroguanidine derivative     

PALB2 Regulates Recombinational Repair through Chromatin Association and Oligomerization

Maintenance of genomic stability ensures faithful transmission of genetic information and helps suppress neoplastic transformation and tumorigenesis. Although recent progress has advanced our understanding of DNA damage checkpoint regulations, little is known as to how DNA repair, especially the RAD51-dependent homologous recombination repair pathway, is executed in vivo. Here, we reveal novel properties of the BRCA2-associated protein PALB2 in the assembly of the recombinational DNA repair machinery at DNA damage sites. Although the chromatin association of PALB2 is a prerequisite for subsequent BRCA2 and RAD51 loading, the focal accumulation of the PALB2·BRCA2·RAD51 complex at DSBs occurs independently of known DNA damage checkpoint and repair proteins. We provide evidence to support that PALB2 exists as homo-oligomers and that PALB2 oligomerization is essential for its focal accumulation at DNA breaks in vivo. We propose that both PALB2 chromatin association and its oligomerization serve to secure the BRCA2·RAD51 repair machinery at the sites of DNA damage. These attributes of PALB2 are likely instrumental for proficient homologous recombination DNA repair in the cell.Fanconi anemia is a rare disease in which patients are prone to the development of childhood aplastic anemia and cancer as well as other congenital defects. Cellular phenotypes of FA⁴ patients are also characterized by their hypersensitivity toward DNA-cross-linking agents, such as mitomycin C (MMC) or cisplatin. Accordingly, MMC treatment greatly induces aberrant chromosomal structures in cells derived from FA patients, including chromosome breakage and chromatin interchanges. Thus, genomic instability is considered as one of the fundamental causes responsible for the clinical and cellular phenotypes observed among FA patients.In human cells two major repair pathways are employed to repair DSBs, namely the homologous recombination (HR) and the non-homologous end-joining pathways. The use of the sister chromatid as information donor during repair renders HR a largely faithful mechanism (1), whereas non-homologous end-joining often leads to genetic mutations because of the gain or loss of genetic information (2).Mounting evidence suggests a functional connection between the 13 FA-complementation group genes (FA-A, B/FAAP95, C, D1/BRCA2, D2, E, F, G/XRCC9, I, J/BACH1, L/PHF9/FAAP43, M/Hef/FAAP250, and N/PALB2) and the DNA repair pathway (3). Recent studies revealed that eight of the FA proteins form a complex to facilitate the ubiquitylation of FANCD2 and FANCI; however, mechanistically how they affect DNA repair remains elusive. Importantly, the identification of the FANCJ/BACH1, FANCD1/BRCA2, and FANCN/PALB2 proteins as components of the HR machinery further support the notion that FA mutations result in DNA repair defects (3–7).Genetics and biochemical studies have shown that the FANCD1 product, BRCA2, facilitates the assembly of RAD51 onto ssDNA substrates, forming a nucleoprotein filament (8–10) that catalyzes DNA strand invasion and D-loop formation. Accordingly, abrogation of FANCD1/BRCA2 function abolishes focal accumulation of RAD51 at DNA breaks. The recent identification of FANCN/PALB2 as the Partner and Localizer of BRCA2 (11) indicated that, much like the damage-signaling pathway, a hierarchical relationship exist for the HR pathway. PALB2 is essential for the focal accumulation of BRCA2 and RAD51 at DSBs. Moreover, PALB2 depletion compromised HR repair and cell survival in response to genotoxic stress (11). Similarly, HR defects and hypersensitivity to cross-linking agents are restored in FANCN/PALB2 patient cells by reconstitution or spontaneous reversion of PALB2, indicating that PALB2 dysfunction is responsible for this FA subtype (12). Moreover, inactivation of PALB2 has also been implicated in breast cancer predisposition, as truncation mutations of PALB2 are found in familial breast cancer cases with intact BRCA1 and BRCA2 (13–15). PALB2 mutations are also associated with an elevated frequency of prostate and colorectal cancers, although the role of PALB2 in the suppression of these cancer types requires further exploration (14, 16). Nevertheless, these human genetic studies provide strong evidence to support that PALB2 plays a critical role in HR repair and is important for the maintenance of genomic integrity and tumor suppression.Given the intimate relationship between PALB2 and HR repair, we decided to examine mechanistically how PALB2 regulates the BRCA2-RAD51-dependent DNA repair events. Interestingly, we found an oligomerization domain on PALB2 and provide evidence to support that PALB2 focal accumulation at the site of DNA damage requires its oligomerization property. Together with its chromatin associating ability, PALB2 initiates recombinational repair at DSBs via the coordination of BRCA2 and RAD51 association with chromatin and the concentration of the repair complex at sites of DNA breaks.     

Physicochemical features of ultra-high viscosity alginates

The physicochemical characteristics of the ultra-high viscosity and highly biocompatible alginates extracted from Lessonia nigrescens (UHV_N) and Lessonia trabeculata (UHV_T) were analyzed. Fluorescence and ¹H NMR spectroscopies, viscometry, and multi-angle light scattering (MALS) were used for elucidation of the chemical structure, molar mass, and coil size. The sequential structures from NMR spectroscopy showed high guluronate content for UHV_T, but low for UHV_N. Intrinsic viscosity [η] measurements exhibited unusual high values (up to 2750 mL/g), whereas [η] of a commercial alginate was only about 970 mL/g. MALS batch measurements of the UHV-alginates yielded ultra-high values of the weight average molar mass (M_w up to 1.1 × 10⁶ g/mol) and of the z-average gyration radius (〈R_G〉_z up to191 nm). The M_w and 〈R_G〉_z distributions of UHV-alginates and of ultrasonically degraded fractions were determined using size exclusion chromatography combined with MALS and asymmetrical flow-field-flow fractionation. The M_w dependency of [η] and 〈R_G〉_z could be described by [η] = 0.059 ×  and 〈R_G〉_z = 0.103 × . (UHV_N: x = 0.52; UHV_T: x = 0.53) indicating that the monomer composition has no effect on coil expansion. Therefore, the equations can be used to calculate M_w and 〈R_G〉_z values of UHV_T- and UHV_N-alginate mixtures as used in immunoisolation. Furthermore, the simple and inexpensive capillary viscometry can be used for real-time validation of the extraction and purification process of the UHV-alginates.