Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects

Through the development of a procedure to measure when hydrogen bonds form under two-state folding conditions, alpha-helices have been determined to form proportionally to denaturant-sensitive surface area buried in the transition state. Previous experiments assessing H/D isotope effects are applied to various model proteins, including lambda and Arc repressor variants, a coiled coil domain, cytochrome c, colicin immunity protein 7, proteins L and G, acylphosphatase, chymotrypsin inhibitor II and a Src SH3 domain. The change in free energy accompanied by backbone deuteration is highly correlated to secondary structure composition when hydrogen bonds are divided into two classes. The number of helical hydrogen bonds correlates with an average equilibrium isotope effect of 8.6 +/- 0.9 cal x mol(-1) x site(-1). However, beta-sheet and long-range hydrogen bonds have little isotope effect. The kinetic isotope effects support our hypothesis that, for helical proteins, hydrophobic association cannot be separated from helix formation in the transition state. Therefore, folding models that describe an incremental build-up of structure in which hydrophobic burial and hydrogen bond formation occur commensurately are more consistent with the data than are models that posit the extensive formation of one quantity before the other.     

Effects of static stress on the mechanical properties of cultured collagen fascicles from the rabbit patellar tendon

In-vitro tissue culture experiments were performed to study the effects of static stress on the mechanical properties of collagen fascicles obtained from the rabbit patellar tendon. After collagen fascicles having the diameter of approximately 300 microm were cultured for 1 and 2 wk under static stress between 0 and 3 MPa, their mechanical properties and crimp morphology were determined using a micro-tensile tester and a light microscope, respectively. The tensile strength and tangent modulus of the fascicles were significantly decreased by culture under no load compared to control fascicles. A statistically significant correlation, which was described by a quadratic curve, was observed between applied stress and tensile strength. The maximum tensile strength (16.7 MPa) was obtained at the applied stress of 1.2 MPa; the strength was within a range of control values. There was a similar correlation between applied stress and tangent modulus, and the modulus was maintained at control level under 1.3 MPa stress. The stress of 1.2 to 1.3 MPa is equivalent to approximately 50 percent of the peak stress developed in the intact rabbit patellar tendon by running. Strain at failure of cultured collagen fascicles was negatively correlated with applied stress, and that at 1.2 to 1.3 MPa stress was almost the same as the control value. Crimp morphology in the fascicles cultured under about 1.2 MPa stress was similar to that in control fascicles. These results indicate that cultured collagen fascicles change the mechanical properties and structure in response to static tensile stress. In addition, their mechanical properties and structure are maintained at control level if the static stress of 50 percent of in-vivo peak stress is applied.     

Seasonal changes in the microbial community of a salt marsh, measured by phospholipid fatty acid analysis

Microbial activity within the environment can have distinct geochemicaleffects, and so changes in a microbial community structure can result ingeochemical change. We examined seasonal changes in both the microbialcommunityand the geochemistry of an inter-tidal salt marsh in north-west England tocharacterise biogeochemical processes occurring at this site.Phospholipid fatty acid (PLFA) analysis of sediment samples collected atmonthly intervals was used to measure seasonal changes in microbial biomass andcommunity structure. The PLFA data were analysed using multivariate techniques(Ward's method and the Mahalanobis distance metric), and we show that the useofthe Mahalanobis distance metric improves the statistical analysis by providingdetailed information on the reasons samples cluster together and identifyingthedistinguishing features between the separate clusters. Five clusters of likesamples were defined, showing differences in the community structure over thecourse of a year.At all times, the microbial community was dominated by PLFA associated withaerobic bacteria, but this was most pronounced in summer (August). Theabundanceof branched fatty acids, a measure of the biomass of anaerobes, started toincrease later in the year than did those associated with aerobes and thefungalbiomarker 18:26 showed a brief late-summer peak.The salt marsh remained mildly oxic throughout the year despite the increase inmicrobial respiration, suggested by the large increases in the abundance ofPLFA, in the warmer months. The conditions therefore remained most favourablefor aerobic species throughout the year, explaining their continual dominanceatthis site. However, as the abundance of PLFA synthesised by anaerobesincreased,increases in dissolved Mn concentrations were observed, which we suggest weredue to anaerobic respiration of Mn(IV) to Mn(II). Overall, the geochemicalconditions were consistent with the microbial community structure and changeswithin it.     

Changes in LPLa and reverse cholesterol transport variables during 24-h postexercise period

We investigated the time course of exercise-induced lipoprotein lipase activity (LPLa) and reverse cholesterol transport (RCT) during the 24-h postexercise period. Subjects were 10 sedentary normolipidemic males [NTG; fasting triglyceride (TG) = 89.1 +/- 8.6 mg/dl] and 6 hyperlipidemic males (HTG; fasting TG = 296.8 +/- 64.0 mg/dl). Each subject performed a control trial (no exercise) and 4 exercise trials. In the exercise trials, a subject jogged on a treadmill at 60% of his maximal O(2) consumption for 1 h. Pre- and postheparin blood samples were taken before exercise (baseline) and at 4, 8, 12, and 24 h after exercise. There was no group difference in LPLa (P > 0.05) over the time points. When the LPLa data from the two groups were combined, LPLa at 24 h after exercise was higher than baseline or at 4, 8, 12 h after exercise (P < 0.05). Plasma TG and lecithin-cholesterol acyltransferase activity (LCATa) were higher in HTG than in NTG, and the total high-density lipoprotein-cholesterol (HDL(tot)-Chol) was lower in HTG than in NTG (P < 0.05). HDL(2)-Chol, LCATa, and cholesterol ester transfer protein activity did not differ during the 24-h postexercise period (P > 0.05). These results suggest that LPLa is still increasing 24 h after an acute aerobic exercise and that the magnitude of the increase in exercise-induced LPLa in HTG was similar to that in NTG. Furthermore, in the sedentary population with or without HTG, the variables related to RCT do not change during the 24-h period after exercise.     

Anti-bovine rhodopsin monoclonal antibody recognizing light-dependent structural change

The antigenic structure of the bovine rhodopsin molecule was investigated by using a bovine rhodopsin-specific monoclonal antibody designated Rh 29. Competition assay with sealed intact disks and broken disks indicated that the antibody-binding region was localized in the intradiscal surface. An antigenic peptide obtained by a cyanogene bromide cleavage of rhodopsin was purified and determined as residues 2-39 in the amino acid sequence. Further analysis suggested that the antigenic determinant included at least residues 21-25. These results were consistent with the structural model for membrane topology of rhodopsin. The antigenicity of the rhodopsin was compared among several states. The antibody bound to both ammonyx LO-solubilized unbleached and bleached rhodopsin. In contrast, upon membrane-embedded rhodopsin, unbleached one was 100-times less antigenic than bleached one. The results suggested that the segment around the determinant of membrane-embedded rhodopsin should undergo a structural change upon absorption of light. Rh 29 detected a band corresponding to bovine, porcine and octopus opsins in immunoblotting. Protein blot of crayfish rhabdome did not show any reactive band. These bands except for crayfish reacted with concanavalin A as well. The N-terminal structure may, therefore, conserved between mammal and erthropoda and diverge between them and cepharopoda.     

Concomitant presence of N-nitroso and S-nitroso proteins in human plasma

Nitric oxide (NO)-mediated nitrosation reactions are involved in cell signaling and pathology. Recent efforts have focused on elucidating the role of S-nitrosothiols (RSNO) in different biological systems, including human plasma, where they are believed to represent a transport and buffer system that controls intercellular NO exchange. Although RSNOs have been implicated in cardiovascular disease processes, it is yet unclear what their true physiological concentration is, whether a change in plasma concentration is causally related to the underlying pathology or purely epiphenomenological, and to what extent other nitrosyl adducts may be formed under the same conditions. Therefore, using gas phase chemiluminescence and liquid chromatography we sought to quantify the basal plasma levels of NO-related metabolites in 18 healthy volunteers. We find that in addition to the oxidative products of NO metabolism, nitrite (0.20 +/- 0.02 micromol/l nitrite) and nitrate (14.4 +/- 1.7 micromol/l), on average human plasma contains an approximately 5-fold higher concentration of N-nitroso species (32.3 +/- 5.0 nmol/l) than RSNOs (7.2 +/- 1.1 nmol/l). Both N- and S-nitroso moieties appear to be associated with the albumin fraction. This is the first report on the constitutive presence of a high-molecular-weight N-nitroso compound in the human circulation, raising the question as to its origin and potential physiological role. Our findings may not only have important implications for the transport of NO in vivo, but also for cardiovascular disease diagnostics and the risk assessment of nitrosamine-related carcinogenesis in man.     

Interaction of plexin-B1 with PDZ domain-containing Rho guanine nucleotide exchange factors

The Rho family GTPase has been implicated in plexin-B1, a receptor for Semaphorin 4D (Sema4D), mediating signal transduction. Rho may also play a function in this signaling pathway as well as Rac, but the mechanisms for Rho regulation are poorly understood. In this study, we have identified two kinds of PDZ domain-containing Rho-specific guanine nucleotide exchange factors (RhoGEFs) as proteins interacting with plexin-B1 cytoplasmic domain. These PDZ domain-containing RhoGEFs showed significant homology to human KIAA0380 (PDZ-RhoGEF) and LARG (KIAA0382), respectively. Both KIAA0380 and LARG could bind plexin-B1 and a deletion mutant analysis of plexin-B1, KIAA0380 and LARG revealed that KIAA0380 and LARG bound plexin-B1 cytoplasmic tail through their PDZ domains. The tissue distribution analysis indicated that plexin-B1 was co-localized with KIAA0380 and LARG in various tissues. Immunocytochemical analysis showed that LARG was recruited to plasma membrane by plexin-B1. These results suggest that PDZ domain-containing RhoGEFs play a role in Sema4D-plexin-B1 mediating signal transduction.     

Arg tyrosine kinase is involved in homologous recombinational DNA repair

c-Abl plays important roles in cellular response to DNA damage. However, possible roles for Arg (Abl-related gene) in DNA damage response are unknown. Here, we show that ionizing radiation (IR)-induced Rad51 focus formation is reduced in Arg-deficient cells generated from a chicken B cell line by targeted disruption. This is consistent with the findings that Arg-deficient cells display hypersensitivity to IR, elevated frequencies of IR-induced chromosomal aberrations, and reduced targeted integration frequencies. All of these abnormalities in DNA damage repair are also observed in ATM-deficient cells but not in c-Abl-deficient cells. Finally, we show that Arg interacts with and phosphorylates Rad51 in 293T cells. These results suggest that Arg plays a role in homologous recombinational (HR) DNA repair by phosphorylating Rad51.     

Comparative genome analysis of potential regulatory elements in the ABCG5-ABCG8 gene cluster

The excretion of sterols from the liver and intestine is regulated by the ABCG5 and ABCG8 transporters. To identify potential regulatory elements, 152 kb of the human ABCG5-ABCG8 gene cluster was sequenced and comparative genome analysis was performed. The two genes are oriented in a head-to-head configuration and are separated by a 374-bp intergenic region, which is highly conserved among several species. Using a reporter construct, the intergenic region was found to act as a bidirectional promoter. A conserved GATA site in the intergenic region was shown by site-directed mutagenesis to act as a repressor for the ABCG5 promoter. The intergenic region was also shown to be partially responsive to treatment by LXR agonists. In summary, several potential regulatory elements were found for the ABCG5 and ABCG8 genes, and the intergenic region was found to act as a bidirectional promoter.