PubMed Health⌕ Search

Biomedical subjects

J Ramstein

Publications and source records attributed to J Ramstein.

At least 19 recordsLinked to original sources
PubMed1995

Solvent-induced structural distortions of horse metmyoglobin.

Structural and dynamic constraints produced by the surrounding solvent on the aquometmyoglobin molecule were investigated by means of circular dichroism and Fourier-transform infrared spectroscopies, tritium/hydrogen exchange kinetics and small-angle neutron-scattering experiments. Formamide and ethanol were chosen as cosolvents because they are known to increase and decrease protein activity, respectively. The CD measurements in the Soret region show that no changes occur in the heme molecular structure nor in the protein near the heme. The results of proton-exchange kinetics experiments indicate that the conformational dynamics of aquometmyoglobin is only marginally affected by the cosolvents. However, the small-angle neutron-scattering spectra strongly suggest that these cosolvents induce some distortions of the tertiary conformation. According to the ultraviolet CD and Fourier-transform infrared data, the alteration of the tertiary conformation results from changes in both the number of intrachain hydrogen bonds and the structures of beta turns of type I' for formamide and of type II for either of the two cosolvents. The use of several techniques allows the present approach to demonstrates that the myoglobin structure is extremely sensitive to its environmental conditions.

Animals↗
PubMed1992

A reexamination of the stopped-flow measured hydrogen-deuterium exchange rates in nucleic acid double helices.

Using the deuteration labelling method in conjunction with an improved stopped-flow instrument, we have reexamined the proton exchange process in poly(dA-dT).poly(dA-dT). A single proton exchange class is found with a rate constant at 20 degrees C of 0.4 S-1. This exchange rate is independent of buffer concentration. From the comparison of these results with those obtained in a former study where two rates were measured, it is concluded that the present deuteration signal corresponds to the exchange of the amino protons, whereas the imino proton exchange is not detected.

Buffers↗
PubMed1990

Base pair opening pathways in B-DNA.

Molecular modeling is used to study the opening pathways of bases within a B-DNA oligomer. It is demonstrated that many open states are possible for a single base pair, although a preference for opening towards the major groove of the double helix is found. In addition we show that opening is strongly influenced by the nature of the base involved and is also coupled in many cases to DNA bending.

Base Composition↗
PubMed1988

Energetic coupling between DNA bending and base pair opening.

The pathway for base pair opening within a B-DNA duplex is investigated by theoretical molecular modeling. The results show that the disruption of a single base pair is energetically compatible with the deductions made from hydrogen exchange measurements. In addition, it is found that the opening process is greatly facilitated by DNA bending and that, conversely, once a base pair is disrupted, DNA can bend very easily. It appears that the energetic coupling between these two processes may play an important role in many biological reactions involving nucleic acid distortion.

DNA↗
PubMed1987

Slow exchanging protons in the Z-form of G-C and A-C alternating polymers by using a rapid dialysis method.

Using a dialysis method we have measured the hydrogen exchange (HX) kinetics in poly(dG-dC).poly(dG-dC), poly(dG-m5dC).poly(dG-m5dC), poly(dG-br5dC).poly(dG-br5dC) and platinated poly(dA-br5dC).poly(dG-dT) under experimental conditions in which these polymers adopt the Z-conformation. The latter polymer has one slow exchanging proton with a half-time of about 2 h, whereas the other G-C alternating polymers display a slow class of two protons with exchange half-time of about 6 h. These exchange half-times are independent of ionic strength and of the nature of the salt for all these polymers in the Z-form. The slow proton exchange appears to be strongly correlated to the Z-conformation but rather independent of the Z-DNA sequence. The comparison of the proton exchange rates with the corresponding B in equilibrium Z transition rates is not in favour of the same rate limiting step for both processes.

Circular Dichroism↗
PubMed1986

Guanine and 7-methylguanine amino proton exchange rates as a function of buffer pK: implications for the exchange mechanism.

Using the stopped-flow kinetic method we have measured the deuteration rate of the amino protons in 2'deoxyguanosine 5'monophosphate and 7-methylguanosine 5'monophosphate. For both compounds the exchange rates are accelerated with increasing concentration of a large number of buffers with widely differing pKs. The results obtained, in conjunction with a theoretical model study, give rise to serious doubts concerning the normally accepted mechanism of amino proton exchange involving a pre-protonation at N7.

Buffers↗
PubMed1986

Poly(dA-dT).poly(dA-dT) two-pathway proton exchange mechanism. Effect of general and specific base catalysis on deuteration rates.

The deuteration rates of the poly(dA-dT).poly(dA-dT) amino and imino protons have been measured with stopped-flow spectrophotometry as a function of general and specific base catalyst concentration. Two proton exchange classes are found with time constants differing by a factor of 10 (4 and 0.4 s-1). The slower class represents the exchange of the adenine amino protons whereas the proton of the faster class has been assigned to the thymine imino proton. The exchange rates of these two classes of protons are independent of general and specific base catalyst concentration. This very characteristic behavior demonstrates that in our experimental conditions the exchange rates of the imino and amino protons in poly(dA-dT).poly(dA-dT) are limited by two different conformational fluctuations. We present a three-state exchange mechanism accounting for our experimental results.

Deuterium↗
PubMed1985

"Asymmetric" opening reaction mechanism of Z-DNA base pairs: a hydrogen exchange study.

With the tritium-Sephadex method, the hydrogen-exchange kinetics of the five NH protons of guanine and cytosine residues in Z-form poly(dG-dC) X poly (dG-dC) were measured as a function of temperature and catalyst concentration. Over the measured temperature range from 0 to 34 degrees C, two classes of protons with constant amplitudes are found. The three protons of the fast class, which were assigned to the guanine amino and imino protons, have an exchange half-time in the minute time range (at 20 degrees C the half-time is 2.5 min) and an activation energy of 18 kcal mol-1. Since these two types of protons exchange at the same rate in spite of their grossly different pK values, the exchange of these protons must be limited by the same nucleic acid conformational change. The two cytosine amino protons of the slow class are especially slow with exchange half-times in the hour time range (at 20 degrees C the exchange half-time is 1 h) and the activation energy is 20 kcal mol-1. The exchange of these two protons is not limited by some nucleic acid conformational change as shown by the marked exchange acceleration of these protons upon addition of 0.2 M imidazole. In addition, we have also reexamined the hydrogen-deuterium exchange kinetics of the amino protons of guanosine cyclic 2',3'-monophosphate by a spectral difference method using a stopped-flow spectrophotometer. The measured kinetic process is monophasic with a rate constant of 3 s-1 at 20 degrees C, which is in the same range as the predicted rate constant of the guanine amino protons.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Composition↗
PubMed1985

Effect of B-Z transition and nucleic acid structure on the conformational dynamics of bound ethidium dimer measured by hydrogen deuterium exchange kinetics.

Ethidium dimer is shown to bind by intercalation, almost equally well, to the B and Z form of poly[(dG-m5dC)].poly[(dG-m5dC)], whereas the ethidium monomer shows a strong preference for the B form. The hydrogen-deuterium (H-D) exchange kinetics of the ethidium dimer bound to the B and Z form of poly [(dG-m5dC)].poly[(dG-m5dC)] could then be compared. The kinetics of the H-D exchange were strikingly slower when the dye was bound to Z DNA as compared to B DNA. The exchange kinetics were also modified when ethidium dimer was bound to tRNA and to a triple stranded structure. It is proposed that a dynamic fluctuation at the level of the nucleic acid could modulate the dynamic fluctuation at the level of the bound ligand.

DNA↗
PubMed1983

Dynamic structure of DNA complexes. Fluorometric measurement of hydrogen-deuterium exchange kinetics of dna-bound ethidium dimer and acridine-ethidium dimer.

The hydrogen-deuterium (H-D) exchange kinetics of free and DNA-bound ethidium dimer and acridine-ethidium heterodimer were measured by stopped flow using fluorescence detection. This technique allowed a very accurate measurement of the exchange process. The H-D exchange kinetics were measured in various environments. In some cases, it was observed that the H-D exchange was much faster than the dissociation rate of dimer-DNA complexes. This showed that the exchange was taking place directly from the bound state. Furthermore, the action of a catalyst (imidazolium ion) on the rate of H-D exchange showed that a dynamic structural fluctuation of the ligand in its DNA complex was a necessary step on the exchange process.

Acridines↗
PubMed1982

The B reversible Z transition of poly(dI-br5dC).poly(dI-br5dC). A quantitative description of the Z form dynamic structure.

The study of poly(dI-br5dC).poly(dI-br5dC) films by infrared spectroscopy shows that in low salt concentration, the conformation of this polynucleotide belongs to the B-family and in high salt concentration to the Z-family. 31P nuclear magnetic resonance and circular dichroism confirm the existence of these two forms. By circular dichroism and ultraviolet absorption, it is shown that the equilibrium constant of the B reversible Z transition depends upon temperature. The deuteration rates of exchangeable protons involved in hydrogen bonds between base pairs were deduced from the changes in absorbance near 1700 cm-1. In the B-form, one class of protons is measured with an exchange half-time of 20 minutes. In the Z-form, two classes of protons are measured with very different exchange half-times, the exchange half-time of the slow protons being of the order of 850 minutes. By comparison of these results with those previously obtained for poly(dG-dC).poly(dG-dC), these very slow protons of these two Z-polynucleotides are identified as the cytosine amino protons. A quantitative description of the dynamic structure of the Z-form is presented.

Circular Dichroism↗
PubMed1981

A hydrogen exchange study of Escherichia coli 5S RNA.

Using the tritium Sephadex method, the number of exchangeable protons in E. coli 5S RNA and the kinetics of their exchange reactions have been measured at two different Mg++ concentrations (10(-2) M and 10(-3) M). A quantitative analysis of these results indicates the presence of two classes of protons exchanging with very different rates. The protons of the slow class, not seen in linear molecules of double helical RNA, exchange with a half-time of 0.6 hour and their exchange kinetics are independent of Mg++ concentration. Reduction of the Mg++ concentration from 10(-2) ot 10(-3) M, however, results in a decrease in the number of these exchangeable protons form 26 to 19. Neither the total number, nor the exchange kinetics of the fast protons are affected by this change in Mg++ concentration. Comparison of these results with those previously obtained with tRNA, suggests the presence of a Mg++ dependent tertiary structure in 5S RNA. The number of exchangeable protons obtained from extrapolation of the exchange curves (120 and 126 respectively for 10(-3) and 10(-2) M Mg++ concentration) are compared to the calculated number of exchangeable protons predicted by previous proposed structural models for E.Coli 5S RNA.

Escherichia coli↗
PubMed1981

Tritium exchange on transfer RNA: slowly exchanging protons sensitive to a change in the dihydrouridine stem.

Measurements of tritium exchange on tRNA were made for periods from 0.5 min to 8 hr after separation from labeled solvent. The exchange curve was analysed in terms of three kinetic classes of exchanging protons with half-lives of 5 hr (12 protons), 0.54 hr (37 protons) and about 3.5 min (58 protons) at 0 degrees C in 0.14 M K+/10 mM Mg2+. The behaviour under varying ionic conditions of protons in the slowest exchange class and of some protons in the intermediate class suggests that they are dependent on the tertiary structure of the molecule. Moreover, in the same range of exchange times characteristic of these latter protons, about 9 more protons were observed in the case of a mutant form of tRNA Trp, the UGA-suppressor species, than in the wild-type tRNATrp. These two species differ only in base 24 in the dihydrouridine stem. This dynamic difference between the wild-type and suppressor species may be related to a functionally important difference in coupling between the conformation of the molecule and interactions at the anticodon.

Escherichia coli↗
PubMed1980

Fluorescence relaxation of proflavin-deoxyribonucleic acid interaction. Kinetic properties of a base-specific reaction.

The kinetics of proflavin binding to Micrococcus lysodeicticus deoxyribonucleic acid (DNA [(G-C) content 72%], to Bacillus megaterium DNA [(A-T) content 70%], and to the polydeoxyribonucleotides poly[d(G-C)] and poly[d(A-T)] was studied with fluorescence temperature-jump methods. Poly[d(A-T)] binds proflavin in a two-step reaction with a preequilibrium. Poly[d(G-C)] is characterized by a bimolecular reaction. The binding of acridines to natural DNAs is shown to be characterized by different types of sites whose properties depend on the base composition. The sites have considerable enthalpic differences which result in exchange of dye molecules between them when the temperature is changed. Also, on natural DNAs A-T base pairs are associated with a rapidly equilibrating external complex which is absent or much weaker for G-C base pairs.

Acridines↗