Biomedical subjects

C Di Primo

Publications and source records attributed to C Di Primo.

17 recordsLinked to original sources

PubMed2001

Modulation of RNA function by oligonucleotides recognizing RNA structure.

Numerous RNA structures are responsible for regulatory processes either because they constitute a signal, like the hairpins or pseudoknots involved in ribosomal frameshifting, or because they are binding sites for proteins such as the trans-activating responsive RNA element of the human immunodeficiency virus whose binding to the viral protein Tat and cellular proteins allows full-length transcription of the retroviral genome. Selective ligands able to bind with high affinity to such RNA motifs may serve as tools for dissecting the molecular mechanisms in which they are involved. Such ligands might also constitute prototypes of therapeutic agents when RNA structures play a role in the expression of dysfunctional genes or in the multiplication of pathogens. Different classes of ligands (aminoglycosides, interacalating agents, peptides) are of interest to this aim. However, oligonucleotides deserve particular consideration. They have been extensively used in the frame of the antisense strategy. The apparent simplicity of this rational approach is, at first sight, very attractive. Indeed, numerous successful studies have been published describing the efficient inhibition of translation, splicing, or reverse transcription in cell-free systems, in cultured cells, or in vivo by oligomers complementary to an RNA region. However, RNA structures restrict the access of the target site to the antisense sequence: The competition between the intramolecular association of RNA regions weakens or even abolishes the antisense effect. Various possibilities have been developed to circumvent this limitation. This includes both rational and combinatorial strategies. High-affinity oligomers were designed to invade the RNA structure. Alternatively, triplex-forming oligonucleotides (TFO) and aptamers may recognize the folded RNA motif. Whereas the use of TFOs is rather limited owing to the strong sequence constraints for triple-helix formation, in vitro selection offers a way to explore vast oligoribo or oligodeoxyribo libraries to identify strong, selective oligonucleotide binders. The candidates (aptamers) selected against the TAR RNA element of HIV-1, which form stable loop-loop (kissing) complexes with the target, provide interesting examples of oligonucleotides recognizing a functional RNA structure through an important contribution of tertiary interactions.

Animals↗

PubMed2000

Is a closing "GA pair" a rule for stable loop-loop RNA complexes?

RNA hairpin aptamers specific for the trans-activation-responsive (TAR) RNA element of human immunodeficiency virus type 1 were identified by in vitro selection (Ducongé, F., and Toulmé, J. J. (1999) RNA 5, 1605-1614). The high affinity sequences selected at physiological magnesium concentration (3 mm) were shown to form a loop-loop complex with the targeted TAR RNA. The stability of this complex depends on the aptamer loop closing "GA pair" as characterized by preliminary electrophoretic mobility shift assays. Thermal denaturation monitored by UV-absorption spectroscopy and binding kinetics determined by surface plasmon resonance show that the GA pair is crucial for the formation of the TAR-RNA aptamer complex. Both thermal denaturation and surface plasmon resonance experiments show that any other "pairs" leads to complexes whose stability decreases in the order AG > GG > GU > AA > GC > UA >> CA, CU. The binding kinetics indicate that stability is controlled by the off-rate rather than by the on-rate. Comparison with the complex formed with the TAR* hairpin, a rationally designed TAR RNA ligand (Chang, K. Y., and Tinoco, I. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, 8705-8709), demonstrates that the GA pair is a key determinant which accounts for the 50-fold increased stability of the TAR-aptamer complex (K(d) = 2.0 nm) over the TAR-TAR* one (K(d) = 92. 5 nm) at physiological concentration of magnesium. Replacement of the wild-type GC pair next to the loop of RNA I' by a GA pair stabilizes the RNA I'-RNA II' loop-loop complex derived from the one involved in the control of the ColE1 plasmid replication. Thus, the GA pair might be the preferred one for stable loop-loop interactions.

Adenine↗

PubMed1998

Photoacoustic calorimetry of proteins.

We have described two examples of time-resolved photoacoustic calorimetry for the study of heme protein transient intermediates. Before photoacoustic calorimetry, determining thermodynamic information on short-lived intermediates was difficult. Along with being sensitive to enthalpic and volume changes, photoacoustic calorimetry can detect conformational changes in a time-resolved manner. In complex protein systems, the interpretation of the structural origins of a conformational change is sometimes difficult. Site-directed mutagenesis has been used successfully to identify the residues that play important roles in the ligand binding to both Mb and cytochrome P450cam. In both systems the hydration state of salt bridges gave rise to volume changes that were identified through mutagenesis of the residues involved. With its increasing popularity and the power of site-directed mutagenesis, time-resolved photoacoustic calorimetry is fast becoming a technique to probe conformational dynamics in proteins.

Acoustics↗

PubMed1997

Dynamics of carbon monoxide binding with cytochromes P-450.

The dynamics of CO rebinding with cytochromes P-450cam, P-450scc, and P-450LM2 after laser flash photolysis have been investigated from 293 to 77 K, and the distribution functions of the rate parameters P(k) and of the activation enthalpy P(H) were determined using the maximum entropy method. In a fluid solvent, geminate rebinding is nonexponential, presumably because of a spectral shift induced by protein relaxation on the same time scale. Substrate binding increases the yield of the bimolecular process and decreases the bimolecular rate by 1 or 2 orders of magnitude. The amplitude of these effects seems to correlate with substrate specificity. In a rigid environment at low temperature, cytochromes P-450 exhibit a bimodal distribution of activation enthalpy; P(H) consists of two distinct bands which are in a thermal equilibrium even at 77 K. The results lead to a scheme in which a common structural perturbation splits the conformational substates of cytochromes P-450 into pairs of "doublet" substates with different dynamic properties. The hierarchy of conformational substates of cytochromes P-450 thus contrasts with that of oxygen-binding hemoproteins such as myoglobin.

Adrenal Cortex↗

PubMed1997

Origin of the photoacoustic signal in cytochrome P-450cam: role of the Arg186-Asp251-Lys178 bifurcated salt bridge.

The origin of the photoacoustic signal in ferrous CO-camphor-cytochrome P-450cam was investigated. Recently, the Arg186-Asp251-Lys178 bifurcated salt bridge, located above the heme pocket, has been shown to play a key role in the control of the diffusion step of camphor binding [Deprez, E., Gerber, N. C., Di Primo, C., Douzou, P., Sligar, S. G., & Hui Bon Hoa, G. (1994) Biochemistry 33, 14464-14468]. We considered the hypothesis that electrostriction resulting from the transient exposure of these charged residues to the solvent could be responsible for part of the photoacoustic signal. We thus examined the effects of a site-directed mutation of these linkages and ionic strength increases. Upon replacement of the Asp251 residue by an asparagine residue, the overall enthalpy and volume change of the CO dissociation reaction decrease from -5 to -24 kcal/mol and from 11 to 5.4 mL/mol, respectively. The mutation has the same effect on the thermodynamic parameters as increasing the ionic strength of the medium over a range of potassium or sodium concentrations from 0 to 500 mM. For the D251N mutant, the overall enthalpy of the reaction does not change with the ionic strength whereas a small effect is observed on the volume change. The results indicate that electrostriction around the bifurcated salt bridge contributes to the photoacoustic signal and suggest a scheme in which, following photodissociation of CO and diffusion of the molecule through the protein matrix, the structure relaxes and the bifurcated salt bridge desolvates.

Camphor↗

PubMed1995

Measurements of CO geminate recombination in cytochromes P450 and P420.

The kinetics of CO geminate recombination in cytochrome P450cam are studied at room temperature subsequent to laser photolysis. The geminate rebinding kinetics of P450 are strongly affected by the presence of the camphor substrate. We observe a approximately 2% geminate yield for substrate-bound P450 and a 90% geminate yield when the substrate is absent. The drastic difference in the geminate kinetics suggests that the presence of camphor significantly alters the CO rebinding and escape rates by modifying the heme pocket environment. Two geminate phases and two bimolecular rebinding phases in the substrate free protein were observed, which could arise from slowly interconverting protein conformations. When the temperature or the viscosity of the solution is changed, the fast geminate rate remains the same, whereas the slow geminate rate and the two bimolecular rates change significantly. The geminate rebinding yield of substrate-free P420 is smaller than that of substrate free P450, but its geminate rebinding rate is faster. This demonstrates that in the absence of substrate, CO escapes from the pocket of P420 much more rapidly than from P450 and suggests that the distal pocket environment is altered in the P420 form.

Carbon Monoxide↗

PubMed1995

Antagonistic effects of hydrostatic pressure and osmotic pressure on cytochrome P-450cam spin transition.

The combined effects of hydrostatic pressure and osmotic pressure, generated by polyols, on the spin equilibrium of fenchone-bound cytochrome P-450cam were investigated. Hydrostatic pressure indices a high spin to low spin transition, whereas polyols induce the reversed reaction. Of the four solutes used, glycerol, glucose, stachyose, and sucrose, only the last two would act on the spin transition by osmotic stress. The spin volume changes measured by both techniques are different, 29 and -350 ml/mol for hydrostatic pressure and osmotic pressure, respectively. It suggests that even if the two are perturbing water molecules, different properties are probed. From the volume change induced by osmotic stress, 19 water molecules are deduced that would be implicated in the spin transition of the fenchone-bound protein. This result suggests that water molecules other than the well defined ones located in the active site play a key role in modulating the spin equilibrium of cytochrome P-450cam.

Camphor 5-Monooxygenase↗

PubMed1994

Electrostatic control of the substrate access channel in cytochrome P-450cam.

Camphor binding to ferric cytochrome P-450cam is a two-step process. The first step corresponds to the diffusion of camphor into the heme pocket, and the second one corresponds to an observable spin transition of the heme iron. In this paper, electrostatic interactions that may control the opening of the structure to allow substrate access to the buried and not solvent-exposed active site were examined. The electrostatic interactions occurring at the protein surface were weakened by increasing the ionic strength of the medium with sodium salts and strengthened by decreasing the dielectric constant of the medium with ethylene glycol as a cosolvent. The results obtained with the wild-type protein were compared to those obtained with the site-directed mutant of cytochrome P-450cam in which the Arg 186-Asp 251 and Lys 178-Asp 251 salt bridges, located at the entrance of the proposed access channel, were suppressed by replacing Asp 251 with an asparagine residue. Over a range of sodium chloride concentrations from 0 to 400 mM, camphor binding is favored, as seen in the variation in the first step dissociation equilibrium constant, K1d, which decreases from 49.5 to 24 microM, respectively. Addition of ethylene glycol favors the dissociation of the substrate-bound complex. The addition of sodium to the ethylene glycol-containing samples reverses the effect of the cosolvent. Removal of the Arg 186-Asp 251 and Lys 178-Asp 251 salt bridges results in an alteration in camphor binding in which K1d is equal to 34 microM without sodium.(ABSTRACT TRUNCATED AT 250 WORDS)

Binding Sites↗

PubMed1994

Effects of monovalent cations on cytochrome P-450 camphor. Evidence for preferential binding of potassium.

Binding of monovalent cations of increasing ionic radius to ferric cytochrome P-450cam was measured. Potassium has the highest affinity for the cation binding site observed in the X-ray crystallographic structure with Kdcat = 12 mM, compared with the smaller cation lithium, (Kdcat = 37 mM) and the larger cation cesium (Kd cat = 20 mM). Coupling between cation binding and camphor binding is established by the observation of a linear relationship between the corresponding binding free energies. Potassium binding favours a conformational change of tyrosine 96 which increases the affinity of the protein for camphor and fully dehydrates the active site.

Binding Sites↗

PubMed1993

Conformational dynamics of cytochrome P-450cam as monitored by photoacoustic calorimetry.

Conformational transitions of cytochrome P-450cam following the dissociation of CO from the ferrous heme were investigated by using photoacoustic calorimetry. The effect of substrate association on the acoustic signal was also examined. Results show that the conformational dynamics of cytochrome P-450cam substrate-free protein occur faster than 10 ns, which is the time scale of the instrument response. The enthalpy and volume change for the dissociation reaction are 2.2 kcal mol-1 and 1.8 mL mol-1, respectively. Upon addition of camphor, the reaction is markedly slowed. An intermediate is formed whose lifetime is 130 ns at 17 degrees C. The overall enthalpy and volume changes are -15.9 kcal mol-1 and 10.3 mL mol-1, respectively. These results, together with published transient Raman spectra [Wells, A. V., Pusheng, L., Champion, P. M., Martinis, S. A., & Sligar, S. G. (1992) Biochemistry 31, 4384-4393] suggest that camphor leaves the heme pocket concomitant with the photoinduced expulsion of CO into the solvent and induces a considerable conformational change in the protein.

Calorimetry↗

PubMed1992

A critical role of protein-bound water in the catalytic cycle of cytochrome P-450 camphor.

The rates of NADH oxidation during the hydroxylation of camphor by cytochrome P-450cam were followed in the presence of co-solvents used to increase the osmotic pressure surrounding the protein-bound water. As a result, the measured Vmax decreases independently of the perturbant tested. Roughly 28 molecules of water, involved during the catalytic cycle, are deduced from the variation of Vmax as a function of osmotic pressure. These molecules, in part, could be those present in the cytochrome P-450cam-putidaredoxin interface.

Camphor 5-Monooxygenase↗

PubMed1992

Heme-pocket-hydration change during the inactivation of cytochrome P-450camphor by hydrostatic pressure.

Hydrostatic pressure has been used to convert cytochrome P-450camphor to cytochrome P-420. The latter is an inactivated but soluble and undenaturated form of cytochrome P-450camphor. Using camphor analogues as probes of the active site we show that the inactivation volume change is directly correlated to the initial degree of hydration of the heme pocket. The values range between -73 ml/mol and -197 ml/mol [Di Primo, C., Hui Bon Hoa, G., Douzou, P. & Sligar, S. G. (1990) Eur. J. Biochem. 193, 383-386] for a totally hydrated (substrate-free, low-spin, six coordinated heme iron) and a non-hydrated (camphor-bound, high-spin, five coordinated heme iron) heme pocket. These results suggest that the larger value, -197 ml/mol, for the inactivation volume change is due to a hydration change of the heme pocket resulting from the displacement of the substrate during the compression and the subsequent entrance of water molecules. Similarly, the stability of the protein against compression is correlated with water accessibility to the active site. Increase in substrate mobility by loss of specific interactions with both regions of well defined secondary structure of cytochrome P-450camphor results in an increase of water accessibility and decrease of stability. Thus for camphor and adamantanone which strongly interact with the protein and exclude water from the active site [Poulos, T. L., Finzel, B. C. & Howard, A. J. (1987) J. Mol. Biol. 195, 687-700; Raag, R. & Poulos, T. L. (1989) Biochemistry 28, 917-922] the increase in stability compared to the free protein is roughly 30 kJ/mol at 20 degrees C. With smaller substrates such as norcamphor, which loosely fits into the active site and does not completely exclude water [Raag, R. & Poulos, T. L. (1989) Biochemistry 28, 917-922], the increase in stability is only 7 kJ/mol. Finally these results suggest that cytochrome P-420 induced by hydrostatic pressure is a unique form where the active site is hydrated and camphor is displaced from its binding site.

Camphor 5-Monooxygenase↗

PubMed1990

Effect of the tyrosine 96 hydrogen bond on the inactivation of cytochrome P-450cam induced by hydrostatic pressure.

The effects of removal of the tyrosine 96 hydrogen bond on the stability and conformational events of cytochrome P-450cam are presented in this communication. Hydrostatic pressure has been used as a tool to perturbe the structure leading to the formation of cytochrome P-420, an inactivated but soluble and undenatured form of the enzyme. We show that the spin transition of cytochrome P-450cam, which is known to be influenced by hydrostatic pressure, is affected by this single mutation. The free energy of stabilisation of native substrate-free cytochrome P-450cam is not affected by the removal of the tyrosine 96 hydrogen bond via mutagenesis to phenylalanine, whereas the substrate-bound protein shows a difference of 21 kJ/mol. These results, as well as an observed 110 ml/mol difference for the volume of the inactivation reaction between substrate-bound native and mutant proteins, have been interpreted in terms of a more hydrated heme pocket for the site-directed mutant at position 96 compared to the wild-type protein where camphor is tightly bound via the tyrosine 96 hydrogen bond and water excluded from the active site.

Camphor↗

PubMed1990

The formation of cytochrome P-450 from cytochrome P-420 is promoted by spermine.

This paper is concerned with camphor-bound bacterial cytochrome P-450 and processes that alter its spin-state equilibrium and influence its transition to the nonactive form, cytochrome P-420, as well as its renaturation to the native camphor-bound cytochrome P-450. Spermine, a polycation carrying a charge of 4 +, and potassium, a monovalent cation, were shown to differently cause an increase of high-spin content of camphor-bound cytochrome P-450. The spermine-induced spin transition saturates around 75% of the high spin; a further addition of KCl to the spermine-containing sample shifted the spin state to 95% of the high spin. The volume change of these spin transitions as measured by the use of high pressure indicated an excess of -40 mL/mol for the sample containing potassium as compared to that containing spermine. These results suggest that the proposed privileged site for potassium has not been occupied by spermine and that pressure forces both the camphor and the potassium ion from its sites, allowing solvent movement into the protein as well as ordering of solvent by the excluded camphor and potassium. Cytochrome P-420 was produced from cytochrome P-450 by hydrostatic pressure in the presence of potassium, spermine, and cysteine. Potassium cation shows a bigger effect on the stability of cytochrome P-450 than spermine or cysteine, as revealed by a higher value of the pressure of half-inactivation, P1/2, and a bigger inactivation volume change. However, potassium cation did not promote renaturation of cytochrome P-420 to cytochrome P-450 while the presence of spermine did.(ABSTRACT TRUNCATED AT 250 WORDS)

Binding Sites↗

PubMed1990

Mutagenesis of a single hydrogen bond in cytochrome P-450 alters cation binding and heme solvation.

Cytochrome P-450cam, a monoxygenase responsible for the regiospecific hydroxylation of camphor, binds its substrate through complimentary van der Waals contacts and the formation of a single hydrogen bond between tyrosine 96 and the ketone group of camphor. Substrate association is positively regulated through the binding of a monovalent cation and the oxidation-reduction potential modulated by the spin state of the ferric heme controlled by water access to the sixth coordination site of the iron. Removal of this single hydrogen bond via site-directed mutagenesis of tyrosine 96 to phenylalanine 96 defines this aspect of the protein structure as responsible for the linkage between cation and substrate cooperativities, the degree of spin state conversion resulting from water access via macromolecule and substrate dynamics, and suggests a specific location for the cation binding site.

Camphor↗

PubMed1989

Conformational changes of cytochromes P-450cam and P-450lin induced by high pressure.

Absorbance and fluorescence spectra of bacterial cytochrome P-450cam and cytochrome P-450lin have been studied as a function of pressure. These pressure-induced spectral perturbations fall into two categories, which are interpreted as resulting from denaturation domains and are discussed in terms of protein structural dynamics. The results presented herein support a view that these two bacterial cytochromes have large structural differences and suggest a picture in which the gellike cortex of each protein may play an essential role in stability and function.

Camphor↗

PubMedDate not supplied

RNA and N3'-->P5' kissing aptamers targeted to the trans-activation responsive (TAR) RNA of the human immunodeficiency virus-1.

We used in vitro selection to identify RNA aptamers able to selectively bind to the TAR RNA motif of HIV-1, an unperfect RNA hairpin involved in the transcription of the retroviral genome. We selected aptameric RNA hairpins giving rise to kissing complexes with TAR. The N3'-->P5' phosphoramidate variant of the aptamer bind to TAR with a Kd in the low nanomolar range. However, only the RNA-RNA loop-loop complex is recognized by the Rop protein of E. coli which is specific for kissing complexes.

Bacterial Proteins↗