Combined kinetic and thermodynamic analysis of alpha-helical membrane protein unfolding

The analytical toolkit developed for investigations into water-soluble protein folding has yet to be applied in earnest to membrane proteins. A major problem is the difficulty in collecting kinetic data, which are crucial to understanding any reaction. Here, we combine kinetic and thermodynamic studies of the reversible unfolding of an alpha-helical membrane protein to provide a definitive value for the reaction free energy and a means to probe the transition state. Our analyses show that the major unfolding step in the SDS-induced denaturation of bacteriorhodopsin involves a reduction in alpha-helical structure and proceeds with a large free-energy change; both our equilibrium and kinetic measurements predict that the free energy of unfolding in the absence of denaturant is +20 kcal.mol(-1), with an associated m-value of 25 kcal.mol(-1). The rate of unfolding in the absence of denaturant, k(u)(H(2)O), is surprisingly very slow ( approximately 10(-15) s(-1)). The kinetics also give information on the transition state for this major unfolding step, with a value for beta (m(f)/[m(f) + m(u)]) of approximately 0.1, indicating that the transition state is close to the unfolded state. We thus present a basis for mapping the structural and energetic properties of membrane protein folding by mutagenesis and classical kinetics.     

Triple-helix formation on ribosome-bound nascent chains of procollagen: deuterium-hydrogen exchange studies.

Polyribosomes containing nascent [3H]proline-labeled collagen chains were isolated from chick embryo fibroblasts in culture. These nascent chains were nearly completely hydroxylated, as indicated by the presence of [3H]hydroxyproline and high hydroxyproline/proline ratios. The polyribosomes were suspended in D2O at 15 degrees and the infrared spectrum was determined using a reference cell containing collagen-depleted polyribosomes in D2O, matched to equal RNA content. The amide I and amide II bands were observed. When the polyribosomes were heated in D2O at 44 degrees in the infrared cells, the N--D amide II absorbance at 1480 cm-1 increased markedly, indicating that H leads to D exchange had occurred. Collagen-depleted polyribosomes showed no such changes in absorbance at 1450-1480 cm-1 upon heating. Polyribosomes recovered from the infrared cells after treatment at 44 degrees and cooling still contained collagen, as indicated by their [3H]hydroxyproline content. These data indicate that nascent collagen bound to the polyribosomes can assume a hydrogen-bonded structure. Taken with prior data showing that the nascent collagen was also resistant to pepsin digestion, it is suggested that the collagen examined is in triple-helix conformation. Because the nascent polyribosome-bound collagen is nearly fully hydroxylated, it must be considered that triple-helix formation can occur between nascent chains while they are attached to the endoplasmic reticulum surface and that chain association and triple-helix formation in vivo may well occur before rather than after release.     

Apolipoprotein E is a kinetic but not a thermodynamic inhibitor of amyloid formation: implications for the pathogenesis and treatment of Alzheimer disease.

The apolipoprotein E4 (APOE4) allele is associated with an early age of onset of the nonfamilial form of Alzheimer disease (AD) and with increased beta protein amyloid deposition in the brain. These two observations may both arise from an effect of the apoE family of proteins on the rate of in vivo amyloidogenesis. We report here that apoE3, the common apoE isoform, is an in vitro amyloid nucleation inhibitor at physiological concentrations. A significant delay in the onset of amyloid fibril formation by the beta-amyloid protein of AD (beta 1-40) was observed at a low apoE3 concentration (40 nM), corresponding to an apoE3/beta protein molar ratio of 1:1000. The inhibitory activity of a proteolytic fragment of apoE3, containing the N-terminal 191 amino acids, is comparable to the native protein, whereas the C-terminal fragment has no activity. ApoE4 is equipotent or slightly less potent than apoE3, which may be due to its inability to form a disulfide dimer, since the apoE3 dimer is a significantly more potent nucleation inhibitor than apoE4. Neither apoE3 nor apoE4 inhibits the seeded growth of amyloid or affects the solubility or structure of the amyloid fibrils, indicating that apoE is not a thermodynamic amyloid inhibitor. We propose that the linkage between the APOE4 allele and AD reflects the reduced ability of APOE4 homozygotes to suppress in vivo amyloid formation.     

Temperature-dependent formation of dimers and oligomers of mitochondrial DNA in cells transformed by a thermosensitive mutant of Rous sarcoma virus

In chick-embryo fibroblasts infected by T5, a temperature-sensitive mutant of Schmidt-Ruppin Rous sarcoma virus, the level of catenated dimeric and oligomeric mitochondrial DNA is temperature-dependent and correlates with the phenotypic manifestation of transformation. At the permissive temperature (36 degrees ), where transformation is expressed, the 2- to 3-fold elevated level characteristic of cells transformed by the wild-type Rous sarcoma virus was observed, but at the nonpermissive temperature (41 degrees ), at which cells appear normal and behave normally, the oligomer level was characteristic of uninfected cells. Temperature shifts from 41 to 36 degrees and vice versa resulted in phenotypic reversion and reversals of the respective levels of multiple-length DNA. Cellular growth rates were not altered. Treatment of control cells with cycloheximide resulted in a 5-fold increase of oligomeric DNA, whereas exposure to 9-beta-D-arabinofuranosyladenine had little effect. With both inhibitors, nuclear but not mitochondrial DNA synthesis was inhibited. The possible relation of formation of oligomeric mitochondrial DNA to alterations in the mitochondrial membranes of transformed cells and to inhibition of protein synthesis in the cytoplasm is discussed.     

Enhanced benzo(a)pyrene metabolism and formation of DNA adducts in monocytes of patients with lung cancer

Summary The conversion of G[³H]benzo(a)pyrene to water-soluble material and to DNA adducts was determined in peripheral blood monocytes of 52 healthy male and female volunteers and 27 patients with lung cancer. Active smokers converted more benzpyrene to DNA-bound material than nonsmokers, but did not form significantly more water soluble material. Monocytes of lung cancer patients clearly formed more water soluble material than cells of the control group, and slightly more DNA adducts when only males are compared. This enhanced BP conversion of lung cancer patients is independent of smoking habits.     

Dynamic metabolic labeling of DNA in vivo with arabinosyl nucleosides

Commonly used metabolic labels for DNA, including 5-ethynyl-2′-deoxyuridine (EdU) and BrdU, are toxic antimetabolites that cause DNA instability, necrosis, and cell-cycle arrest. In addition to perturbing biological function, these properties can prevent metabolic labeling studies where subsequent tissue survival is needed. To bypass the metabolic pathways responsible for toxicity, while maintaining the ability to be metabolically incorporated into DNA, we synthesized and evaluated a small family of arabinofuranosyl-ethynyluracil derivatives. Among these, (2′S)-2′-deoxy-2′-fluoro-5-ethynyluridine (F-ara-EdU) exhibited selective DNA labeling, yet had a minimal impact on genome function in diverse tissue types. Metabolic incorporation of F-ara-EdU into DNA was readily detectable using copper(I)-catalyzed azide–alkyne “click” reactions with fluorescent azides. F-ara-EdU is less toxic than both BrdU and EdU, and it can be detected with greater sensitivity in experiments where long-term cell survival and/or deep-tissue imaging are desired. In contrast to previously reported 2′-arabino modified nucleosides and EdU, F-ara-EdU causes little or no cellular arrest or DNA synthesis inhibition. F-ara-EdU is therefore ideally suited for pulse-chase experiments aimed at “birth dating” DNA in vivo. As a demonstration, Zebrafish embryos were microinjected with F-ara-EdU at the one-cell stage and chased by BrdU at 10 h after fertilization. Following 3 d of development, complex patterns of quiescent/senescent cells containing only F-ara-EdU were observed in larvae along the dorsal side of the notochord and epithelia. Arabinosyl nucleoside derivatives therefore provide unique and effective means to introduce bioorthogonal functional groups into DNA for diverse applications in basic research, biotechnology, and drug discovery.     

Age-dependent changes in rat liver microsomal NADPH cytochrome C (P-450) reductase: a kinetic analysis

Rat liver microsomal NADPH cytochrome c (P-450) reductase (EC 1.6.2.4) exhibits several marked age-dependent changes, including a decline in specific activity, reduced inducibility and enhanced thermostability, which are indicative of an alteration in the quality of this enzyme. The present study examined the kinetic profile of the microsomal-bound enzyme in an effort to further define the effects of aging on the hepatic mixed function oxidase system. Intact microsomes isolated from young adult (3 months), mature (16 months) and senescent (27 months) rats were subjected to an extensive double reciprocal kinetic analysis employing NADPH and cytochrome c as substrates. The Km values obtained with the initial substrate (NADPH) remained unchanged with animal age, whereas there was a decline in this parameter for the artificial acceptor substrate, cytochrome c. The Vmax values for both substrates were reduced as a function of increasing age, perhaps reflecting a concomitant decline in the relative amount(s) of efficient reductase in the microsomes.     

Monte Carlo description of oligoelectrolyte properties of DNA oligomers: range of the end effect and the approach of molecular and thermodynamic properties to the polyelectrolyte limits

Applications of the grand canonical Monte Carlo method demonstrate the importance of end effects on fundamental molecular and thermodynamic properties of oligoelectrolyte solutions. Simulations are carried out for a series of solutions containing double-helical DNA oligomers of varying numbers of phosphate charges N (8 less than or equal to N less than or equal to 100) and univalent electrolyte at fixed activity (a +/- = 1.76 mmol/dm3). These results are used to evaluate as follows: C+N(a), the local concentration of cations at various axial positions along the oligomer surface; C+N(a), the axial average of these concentrations; TN, the preferential interaction coefficient expressed per oligomer charge, which is directly related to the fractional thermodynamic extent of association of counterions. A sufficiently long oligomer (N greater than or equal to 48 under the conditions simulated) is characterized by an interior region over which C+N(a) is uniform and equal to C+ infinity (a), the polyion limit. This interior region is flanked by two symmetric terminal regions, in which C+N(a) varies linearly with axial position from the end of the oligomer to a distance approximately 18 monomer units (approximately 3.1 nm) from that end. For long oligomers, the characteristics of the terminal regions [length and axial profile of C+N(a)] do not vary with N and, by inference, also pertain to the polyion under the same conditions. Both C+N(a) and TN approach their polyelectrolyte limits as linear functions of 1/N. These linear dependences can be attributed to the increasing predominance of the contribution due to the polyion-like interior of the oligomer as N increases.     

Hg(II) binding to a weakly associated coiled coil nucleates an encoded metalloprotein fold: a kinetic analysis

A detailed kinetic analysis of metal encapsulation by a de novo-designed protein is described. The kinetic mechanism of Hg(II) encapsulation in the three-stranded coiled coil formed by the peptide CH(3)CO-G LKALEEK CKALEEK LKALEEK G-NH(2) (Baby L9C) is derived by global analysis. The mechanism involves rapid initial collapse of two peptides by Hg(II) forming Hg(Baby L9C(-H))(2) with a linear thiolato Hg(II) bound to the cysteine sulfur atoms. Here, Baby L9C(-H) denotes Baby L9C with the cysteine thiol deprotonated. Addition of the third peptide, forming the three-stranded coiled coil, is the rate-determining step and results in an intermediate state involving two separate species. One of the species, termed the properly folded intermediate, undergoes rapid deprotonation of the third cysteine thiol, yielding the desired three-stranded coiled coil with an encapsulated trigonal thiolato Hg(II). The other species, termed the misfolded intermediate, rearranges in an experimentally distinguishable step to the properly folded intermediate. The order of the reaction involving the addition of the third peptide with respect to the concentration of Baby L9C indicates that addition of the third helix only occurs through reaction of Hg(Baby L9C(-H))(2) and Baby L9C that is unassociated with a coiled coil. Temperature dependence of the reaction afforded activation parameters for both the addition of the third helix (deltaH = 20(2) kcalmol; deltaS= 40(5) calmol K) and the rearrangement of the misfolded intermediate steps (deltaH = 23(2) kcalmol; deltaS= 27(5) calmol K). The mechanism is discussed with regard to metalloprotein folding and metalloprotein design.     

Steady state of an ATP-driven calcium pump: limitations on kinetic and thermodynamic parameters.

A numerical analysis was carried out to explore limitations on kinetic and thermodynamic parameters for an ATP-driven Ca pump. A conventional pump reaction cycle was employed, with a transport stoichiometry of two Ca ions per cycle. Rigid requirements were imposed to represent the needs of physiological function, defined as the ability to maintain the cytoplasmic Ca concentration below 10(-7) M against a 3 mM concentration on the opposite side of the membrane. Realistic physical limits were placed on the magnitudes of rate constants for individual reaction steps. Reversibility under laboratory conditions was assumed. The results show that these requirements can be satisfied simultaneously only if the equilibrium constant for binding Ca from the cytoplasmic (uptake) side of the membrane is much larger than the binding constant on the discharge side. More generally, the results demonstrate that limitations on rate constants make it possible for the pump to maintain an adequate rate only if steady-state levels of kinetically important (slowly reacting) reaction intermediates do not become too disparate. Experimental data for the sarcoplasmic reticulum calcium pump support these theoretical conclusions.     

Properties of the Escherichia coli DNA Binding (Unwinding) Protein: Interaction with DNA Polymerase and DNA

The E. coli DNA binding protein reduces the activity of the single-strand-specific nucleases associated with all three DNA polymerases known in E. coli. A slight excess of binding protein over that required to saturate the DNA template leads to total inhibition of activity of the 3' --> 5' nucleases associated with DNA polymerases I and III, but restores maximum activity of the DNA polymerase II-associated nuclease. The binding protein forms a specific complex with DNA polymerase II in the absence of DNA, and it is this complex that degrades a DNA.binding protein complex. Binding protein also facilitates the binding of DNA polymerase II to single-stranded DNA, whereas the binding to DNA of DNA polymerase I is inhibited. These data may explain the specificity with which the binding protein enhances the synthetic ability of DNA polymerase II.     

The metabolism of lipoprotein(a) and other apolipoprotein B-containing lipoproteins: a kinetic study in humans

Lipoprotein(a) is a risk factor for cardiovascular disease composed of an apolipoprotein B-containing lipoprotein to which a second protein, apolipoprotein(a), is attached. We investigated in seven subjects with Lp(a) levels of 39--85 mg/dl the metabolism of four apo B-containing lipoproteins (VLDL(1), VLDL(2), IDL and LDL) together with that of apo B and apo(a) isolated from Lp(a). Rates of secretion, catabolism and where appropriate, transfer were determined by intravenous administration of d(3)-leucine, mass spectrometry for measurements of leucine tracer/tracee ratios and kinetic data analysis using multicompartmental metabolic modeling. Apo B in Lp(a) was secreted at a rate of 0.28 (0.17--0.40) mg/kg per day. It was found to originate from two sources -- 53% (43--67) were derived from preformed lipoproteins, i.e. IDL and LDL, the remainder was accounted for by apo B, directly secreted by the liver. The fractional catabolic rates (FCRs) of apo B and of apo(a) prepared from Lp(a) were determined as 0.27 (0.16--0.38) and 0.24 (0.12--0.40) pools per day, respectively, which is less than half of the FCR observed for LDL. Our in vivo data from humans support the view that Lp(a) assembly is an extracellular process and that its two protein components, apo(a) and apo B, are cleared from the circulation at identical rates.     

Response to glucose and lipid infusions in sepsis: a kinetic analysis

The kinetics and oxidation of glucose and free fatty acid (FFA) metabolism were assessed in control and Escherichia coli septicemic dogs by using primed, constant infusions of U-14C-glucose and 1,2, 13C-palmitic acid. In the controls, the infusion of glucose suppressed endogenous glucose production completely, whereas, in the septic dogs, only a 30% suppression of glucose production occurred. The ability of the septic dogs to oxidize endogenous or exogenous glucose was decreased significantly. The basal rate of appearance of FFA was significantly higher in the septic dogs, but their ability to oxidize FFA was comparable to that of the control dogs; therefore, the basal rate of FFA oxidation was higher in the septic dogs. These studies indicate that septic dogs have a decreased capacity to oxidize glucose, but that they retain their ability to oxidize long-chain fatty acids. Because the rate of lipolysis was increased in sepsis, lipid was the predominate energy substrate in this septic model.     

Crucial role for DNA supercoiling in Mu transposition: a kinetic study.

DNA supercoiling plays an indispensable role in an early step of bacteriophage Mu transposition. This step involves formation of a nucleoprotein complex in which the Mu ends synapse and undergo two concerted single-strand cleavages. We describe a kinetic analysis of the role of supercoiling in the Mu-end synapsis reaction as measured by the cleavage assay. We observe a dependence of the reaction rate on superhelical density as well as on the length of Mu donor plasmid DNA. The reaction has a high activation enthalpy (approximately 67 kcal/mol). These results imply that the free energy of supercoiling is used directly to lower the activation barrier of the rate-limiting step of the reaction. Only the free energy of supercoiling associated with DNA outside the Mu ends appears to be utilized, implying that the Mu ends come together before the supercoiling energy is used. Our results suggest an essential function for the bacterial sequences attached to the ends of Mu virion DNA.     

Acetylation of Werner syndrome protein (WRN): relationships with DNA damage,DNA replication and DNA metabolic activities

Loss of Werner syndrome protein function causes Werner syndrome, characterized by increased genomic instability, elevated cancer susceptibility and premature aging. Although WRN is subject to acetylation, phosphorylation and sumoylation, the impact of these modifications on WRN’s DNA metabolic function remains unclear. Here, we examined in further depth the relationship between WRN acetylation and its role in DNA metabolism, particularly in response to induced DNA damage. Our results demonstrate that endogenous WRN is acetylated somewhat under unperturbed conditions. However, levels of acetylated WRN significantly increase after treatment with certain DNA damaging agents or the replication inhibitor HU. Use of DNA repair-deficient cells or repair pathway inhibitors further increase levels of acetylated WRN, indicating that induced DNA lesions and their persistence are at least partly responsible for increased acetylation. Notably, acetylation of WRN correlates with inhibition of DNA synthesis, suggesting that replication blockage might underlie this effect. Moreover, WRN acetylation modulates its affinity for and activity on certain DNA structures, in a manner that may enhance its relative specificity for physiological substrates. Our results also show that acetylation and deacetylation of endogenous WRN is a dynamic process, with sirtuins and other histone deacetylases contributing to WRN deacetylation. These findings advance our understanding of the dynamics of WRN acetylation under unperturbed conditions and following DNA damage induction, linking this modification not only to DNA damage persistence but also potentially to replication stalling caused by specific DNA lesions. Our results are consistent with proposed metabolic roles for WRN and genomic instability phenotypes associated with WRN deficiency.