Proton polarizability and proton transfer in histidine-phosphate hydrogen bonds as a function of cations present: ir investigations

(L -His)_n- dihydrogen phosphate systems are studied by ir spectroscopy in the presence of various cations and as a function of the degree of hydration. Ir continua indicate that (I) OH … N ? O^?…H⁺N (IIR) hydrogen bonds are formed and that these bonds show high proton polarizability, which increases from the Li⁺ to the K⁺ system. In the K⁺?system, His-P_i-P_i chains are formed, showing particularly high proton polarizability due to collective proton motion within both hydrogen bonds. The OH N ? O^?…H^?N equilibria are determined from ir bands. With the Li⁺ system, 55% of the protons are present at the histidine residues; this percentage is smaller with the Na⁺ system (41%), and amounts to only 32% with the K⁺ system. With the increasing degree of hydration the removal of the degeneracy of ν_as?PO^2?₃ vanishes, indicating loosening of the cations from the phosphates. Nevertheless, the hydrogen bond acceptor O atom becomes more negative; a shift of the equilibrium to the right is observed in the OH… N ? O^?…H⁺N bond. This is explained by the strong interaction of the dipole of the hydrogen bonds with the water molecules. All these results show that protons can be shifted easily in these hydrogen bonds due to their high proton polarizability. The transfer equilibria can be controlled easily by local electrical fields. In addition, these results may be of significance when phosphates interact with proteins.     

Proton polarizability of poly(L-tyrosine)–hydrogen phosphate hydrogen bonds as a function of alkali cations

We studied films of poly(L -tyrosine) with hydrogen phosphate (residue/phosphate, 1:1) by ir spectroscopy. The influences of the alkali cations (Li⁺, Na⁺, K⁺) and of the degree of hydration were clarified. If Li⁺ ions are present, the OH ?^?OP hydrogen bonds formed in the dried films between the tyrosine OH groups and hydrogen phosphate are asymmetrical. The formation of hydrogen phosphate–hydrogen phosphate hydrogen bonds is prevented by the presence of the Li⁺ ions. With an increase in the degree of hydration, the tyrosine–phosphate bonds are not broken but become slightly stronger. Completely different behaviour is found if K⁺ ions are present. In dry films, the OH ?^?OP ? O^? ?HOP hydrogen bonds formed between tyrosine and hydrogen phosphate show large proton polarizability. The tyrosine proton has a noticeable residence time at the acceptor O atom of the phosphate. The difference in the behaviour of the system with K⁺ ions when compared to the system with Li⁺ ions can be explained, since the hydrogen acceptor O atom of phosphate ions is more negatively charged due to the weaker influence of the K⁺ ions. Furthermore, POH ?^?OP hydrogen bonds between hydrogen phosphate molecules are formed. With an increase in the degree of hydration, the tyrosine–hydrogen phosphate hydrogen bonds are broken, all tyrosine protons are found at the tyrosine residues, and the -PO₃^? groupings are in a symmetrical environment, indicating that the K⁺ ions are removed from these groupings. If the degree of hydration increases further, hydrogen-bonded systems such as hydrogen phosphate–water–hydrogen phosphate are formed that show large proton polarizability due to collective proton motion. When Na⁺ ions are present, the OH ?^?OP ? O^? ?HOP hydrogen bonds formed in dry films still show proton polarizability, but the residence time of the tyrosine proton at the phosphate is very short.     

Strongly hydrogen-bonded water molecule present near the retinal chromophore of Leptosphaeria rhodopsin, the bacteriorhodopsin-like proton pump from a eukaryote

Leptosphaeria rhodopsin (LR) is an archaeal-type rhodopsin found in fungi, and is the first light-driven proton-pumping retinal protein from eukaryotes. LR pumps protons in a manner similar to that of bacteriorhodopsin (BR), a light-driven proton pump of haloarchaea. The amino acid sequence of LR is more homologous to that of Neurospora rhodopsin (NR) than BR, whereas NR has no proton-pumping activity. These facts raise the question of how the proton-pumping function is achieved. In this paper, we studied structural changes of LR following the retinal photoisomerization by means of low-temperature Fourier transform infrared (FTIR) spectroscopy, and compared the obtained spectra with those for BR and NR. While the light-induced photoisomerization from the all-trans to 13-cis form was commonly observed among LR, BR, and NR, we found that the structural changes of LR are closer to those of BR than to those of NR in terms of detailed vibrational bands of retinal and protein. The most prominent difference was seen for the water O-D stretching vibrations (measured in D2O). LR exhibits an O-D stretch of water at 2257 cm(-1), indicating the presence of a strongly hydrogen-bonded water molecule. Such strongly hydrogen-bonded water molecules (O-D stretch at <2400 cm(-1)) were observed for BR, but not for NR. Comprehensive studies of BR mutants and archaeal rhodopsins have revealed that strongly hydrogen-bonded water molecules are found only in the proteins exhibiting proton-pumping activity, suggesting that strongly hydrogen-bonded water molecules and transient weakening of their binding are essential for the proton-pumping function of rhodopsins. This observation for LR provided additional experimental evidence of the correlation between strongly hydrogen-bonded water molecules and proton-pumping activity of archaeal rhodopsins.     

The F0 complex of the ATP synthase of Escherichia coli contains a proton pathway with large proton polarizability caused by collective proton fluctuation.

The F0 complex of the Escherichia coli ATP synthase embedded into cardiolipin liposomes was studied by FT-IR spectroscopy. For comparison, respective studies were performed with dried F0 liposomes and with F0 liposomes treated with N,N'-dicyclohexyl-carbodiimide (DCCD), which binds to Asp-61 of subunit c. Furthermore, the effect of H2O-->D2O exchange on the infrared spectrum was investigated. With F0 liposomes an infrared continuum is observed beginning at about 3000 cm-1 and extending toward smaller wavenumbers. In the DCCD-treated sample, this continuum is no longer observed. It vanishes also with drying of the liposomes. After H2O-->D2O exchange, this infrared continuum begins at about 2350 cm-1 and is less intense. All of these results demonstrate that a proton pathway in native F0 is present, in which the protons are shifted in a hydrogen-bonded chain with large proton polarizability due to collective proton tunneling. With the D2O-hydrated system, deuteron polarizability due to collective deuteron motion is observed, but the polarizability due to collective deuteron motion is smaller. Such pathways are very efficient, because they conduct protons or deuterons within picoseconds. These pathways lose their polarizability if the F0 complex is blocked by DCCD or if the liposomes are dried. On the basis of our results on the proton polarizability of hydrogen bonds and hydrogen-bonded systems and on the basis of structural data from the literature, the nature of the proton pathway of the F0 complex of E. coli is discussed.     

Photophosphorylation as a function of illumination time. I. Effects of permeant cations and permeant anions

(1) Very brief periods of illumination do not initiate photophosphorylation in isolated chloroplast lamellae. The time of illumination required before any phosphorylation can be detected is inversely proportional to the light intensity. At very high intensities, phosphorylation is initiated after illumination for about 4 ms.(2) There is no similar delay in the initiation of electron transport. The rate of electron transport is very high at first but declines at about the time the capacity for ATP synthesis develops. When the chloroplasts are uncoupled with gramicidin the high initial rate persists.(3) Various ions which permeate the thylakoid membrane (K⁺ or Rb⁺ in the presence of valinomycin, SCN^?, I^?, or ClO₄^?) markedly increase the time of illumination required to initiate phosphorylation. Potassium ions in the presence of valinomycin increase the delay to a maximum of about 50 ms whereas thiocyanate ions increase the delay to a maximum of about 25 ms. The effects of K⁺ with valinomycin and the effect of SCN^? are not additive. Permeant ions and combinations of permeant ions have little or no effect on phosphorylation during continuous illumination.(4) The reason for the threshold in the light requirement and the reason for the effect of permeant ions thereon are both obscure. However, it could be argued that the energy for phosphorylation initially resides in an electric potential gradient which is abolished by migration of ions in the field, leaving a more slowly developing proton concentration gradient as the main driving force for phosphorylation during continuous illumination. If so, the threshold in the presence of permeant ions should depend on internal hydrogen ion buffering.     

Patients' reactions to their investigations: a study of 504 patients.

Five hundred and four patients who had undergone hospital investigations were interviewed to find out how much information they had been given about the tests; their reactions before, during and after the test; and any after effects. In 74% of cases the tests had been satisfactorily explained. Patients were told more about complicated procedures such as cardiac catherisation than about routine ones such as venepuncture or barium meal examinations. The comments doctors made while performing the investigations were generally reassuring and were only rarely worrying or impatient. About half the patients suffered pain or discomfort during the test and rather more complained of after effects. Only 5% of patients said they would refuse the test again, though 36% said they would agree only reluctantly. Communication lies at the heart of the problem. Hospitals should consider issuing handouts on investigations to back up the doctor''s information and to dispel myths. Staff should be more careful in concealing frightening-looking equipment, and if patients have to wait during investigations it may help reduce their anxiety if they are provided with something to occupy their time.     

pK(a) Calculations suggest storage of an excess proton in a hydrogen-bonded water network in bacteriorhodopsin.

Calculations of protonation states and pK(a) values for the ionizable groups in the resting state of bacteriorhodopsin have been carried out using the recently available 1.55 A resolution X-ray crystallographic structure. The calculations are in reasonable agreement with the available experimental data for groups on or near the ion transport chain (the retinal Schiff base; Asp85, 96, 115, 212, and Arg82). In contrast to earlier studies using lower-resolution structural data, this agreement is achieved without manipulations of the crystallographically determined heavy-atom positions or ad hoc adjustments of the intrinsic pK(a) of the Schiff base. Thus, the theoretical methods used provide increased reliability as the input structural data are improved. Only minor effects on the agreement with experiment are found with respect to methodological variations, such as single versus multi-conformational treatment of hydrogen atom placements, or retaining the crystallographically determined internal water molecules versus treating them as high-dielectric cavities. The long-standing question of the identity of the group that releases a proton to the extracellular side of the membrane during the L-to-M transition of the photocycle is addressed by including as pH-titratable sites not only Glu204 and Glu194, residues near the extracellular side that have been proposed as the release group, but also an H(5)O(2)(+) molecule in a nearby cavity. The latter represents the recently proposed storage of the release proton in an hydrogen-bonded water network. In all calculations where this possibility is included, the proton is stored in the H(5)O(2)(+) rather than on either of the glutamic acids, thus establishing the plausibility on theoretical grounds of the storage of the release proton in bacteriorhodopsin in a hydrogen-bonded water network. The methods used here may also be applicable to other proteins that may store a proton in this way, such as the photosynthetic reaction center and cytochrome c oxidase.     

A proton magnetic resonance study of the conformation of methionine-enkephalin as a function of pH.

It is found that methionine-enkephalin has at least two different conformations in aqueous solution, one at low and one at high pH. From inspection of titration curves and coupling constant values, it seems reasonable to conclude that these conformations are characterized by a folding so as to bring the two ends of the molecule in close proximity. This behavior parallels that found recently in (CD3)2SO as the solvent. It follows that the Phe-Met region of the molecule constitutes a relatively rigid region, but that the chain possesses flexibility around the first Gly residue. Possible implications of this behavior with respect to the receptor site are discussed.     

Electric birefringence of restriction enzyme fragments of DNA: optical factor and electric polarizability as a function of molecular weight

The electric birefringence of restriction enzyme fragments of DNA has been investigated as a function of DNA concentration, buffer concentration, and molecular weight, covering a molecular weight range from 80 to 4364 base pairs (bp) (6 × 10⁴–3 × 10⁶ daltons). The specific birefringence of the DNA fragments is independent of DNA concentration below 20 μg DNA/ml, but decreases with increasing buffer concentration, or conductivity, of the solvent. At sufficiently low field strengths, the Kerr law is obeyed for all fragments. The electric field at which the Kerr law ends is inversely proportional to molecular weight. In the Kerr law region the rise of the birefringence is accurately symmetrical with the decay for fragments ≤ 389 bp, indicating an induced dipole orientation mechanism. The optical factor calculated from a 1/E extrapolation of the high field birefringence data is ?0.028, independent of molecular weight; if a 1/E² extrapolation is used, the optical factor is ?0.023. The induced polarizability, calculated from the Kerr constant and the optical factor, is proportional to the square of the length of the DNA fragments, and inversely proportional to temperature. Saturation curves for DNA fragments ≤ 161 bp can be described by theoretical saturation curves for induced dipole orientation. The saturation curves of larger fragments are broadened, because of a polarization term which is approximately linear in E, possibly related to the saturation of the induced dipole in high electric fields. This “saturated induced dipole” is found to be 6400 D, independent of molecular weight. The melting temperature of a 216-bp sample is decreased 6°C in an electric field of 8 kV/cm, because the lower charge density of the coil form of DNA makes it more stable in an electric field than the helix form.     

Mitochondrial oxygen affinity as a function of redox and phosphate potenitals

1. The conditions under which mitochondria might catalyse a net reversal of oxidative phosphorylation are analysed.

2. Rat-liver mitochondria, incubated under such conditions, show a strongly diminished affinity for oxygen.

3. The velocity of respiration under these conditions is a hyperbolic function of the oxygen concentration.

4. The K_m for oxygen is less than 0.1 μM at low phosphate potential, irrespective of substrate, and 1–3 μM under reversal conditions.

5. The observed kinetics can be accounted for in a simple mechanism for cytochrome oxidase action.     

Glutamic acid as a synpatic transmitter candidate in the dorsal sensory neuron: reconsiderations.

Two primary reasons which are emerging to suggest that glutamate is not a dorsal root transmitter are: 1) that free glutamate levels in the dorsal root vs. the ventral root are not sufficiently different to warrant a transmitter function in the dorsal root, and 2) the spinal cord glutamate levels do not significantly change (per g tissue) after dorsal root input section. Recent analyses suggest, however, that there is a highly significant depression of glutamate in the dorsal root when related to total free amino acid concentration changes after root injury. This is not seen in the peripheral nerve. Thus the dorsal vs. ventral root free glutamate concentration difference is highly significant metabolically. The failure to see a decrease in spinal cord gray glutamate levels after dorsal root section would appear to be explained by the fact that the spinal cord satellite cells and neurons have a higher free glutamate concentration than the entering dorsal roots along with a considerable perikaryal free amino acid pool for protein synthesis. This will mask any changes due to dorsal root section.Comparisons of excess free glutamate and substance P (the two leading dorsal root transmitter candidates) in the dorsal root compared to the ventral root have shown that there is a much larger excess of free glutamate in the dorsal root. This is true, even when considering the excitatory potency differences of these two substances. Thus, a very large free glutamate excess in the dorsal root is present with a relatively small concentration difference compared to the ventral root (where a transmitter role is not entertained). This fact could be of considerable metabolic significance in the regulation of transmitter levels of glutamate. The data available, therefore, are supportive of a possible glutamate transmitter role in a population of dorsal root fibers.     

Clotrimazole as a pharmaceutical: past,present and future.

Clotrimazole is a broad‐spectrum antimycotic drug mainly used for the treatment of Candida albicans and other fungal infections. A synthetic, azole antimycotic, clotrimazole is widely used as a topical treatment for tinea pedis (athlete's foot), as well as vulvovaginal and oropharyngeal candidiasis. It displays fungistatic antimycotic activity by targeting the biosynthesis of ergosterol, thereby inhibiting fungal growth. As well as its antimycotic activity, clotrimazole has become a drug of interest against several other diseases such as sickle cell disease, malaria and some cancers. It has also been combined with other molecules, such as the metals, to produce clotrimazole complexes that show improved pharmacological efficacy. Moreover, several new, modified‐release pharmaceutical formulations are also undergoing development. Clotrimazole is a very well‐tolerated product with few side effects, although there is some drug resistance appearing among immunocompromised patients. Here, we review the pharmaceutical chemistry, application and pharmacology of clotrimazole and discuss future prospects for its further development as a chemotherapeutic agent.     

Aspartic acids 96 and 85 play a central role in the function of bacteriorhodopsin as a proton pump.

A spectroscopic and functional analysis of two point-mutated bacteriorhodopsins (BRs) from phototrophic negative halobacterial strains is reported. Bacteriorhodopsin from strain 384 contains a glutamic acid instead of an aspartic acid at position 85 and BR from strain 326 contains asparagine instead of aspartic acid at position 96. Compared to wild-type BR, the M formation in BR Asp85---Glu is accwelerated approximately 10-fold, whereas the M decay in BR Asp96---Asn is slowed down approximately 50-fold at pH6. Purple membrane sheets containing the mutated BRs were oriented and immobilized in polyacrylamide gels or adsorbed to planar lipid films. The measured kinetics of the photocurrents under various conditions agree with the observed photocycle kinetics. The ineffectivity of BR Asp85---Glu resides in the dominance of an inactive species absorbing maximally at approximately 610 nm, while BR Asp96---Asn is ineffective due to its slow photocycle. These experimental results suggest that aspartic acid 96 plays a crucial role for the reprotonation of the Schiff base. Both residues are essential for an effective proton pump.     

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.     

EGF-R as a hemopoietic growth factor receptor: the c-erbB product is present in chicken erythrocytic progenitors and controls their self-renewal.

c-erbB, encoding the EGF receptor (EGF-R), was originally identified as the cellular homolog of a chicken leukemia oncogene. In humans, EGF-R is distributed widely except in hemopoietic tissues, and its amplification is associated with epidermal and glial malignancies. Here we show that c-erbB is present in normal chicken erythrocytic progenitors and transmits the mitogenic signal induced by TGF alpha. Cells that contain high affinity EGF-R are at approximately the BFU-E stage, and their long-term renewal can be induced by TGF alpha. Upon addition of insulin and erythropoietin, they can be induced to terminally differentiate into red cells. We previously demonstrated that v-erbA blocks differentiation of chicken erythrocytic progenitors but does not abrogate their growth factor dependence for proliferation. These data indicate that proliferation and differentiation are not necessarily coupled in these cells. They also demonstrate a direct role of c-erbB in the control of self-renewal of normal chicken erythrocytic progenitors and could account for the predominant leukemogenic potential of the chicken erbB gene.     

Reaction networks as systems for resource allocation: a variational principle for their non-equilibrium steady states

Within a fully microscopic setting, we derive a variational principle for the non-equilibrium steady states of chemical reaction networks, valid for time-scales over which chemical potentials can be taken to be slowly varying: at stationarity the system minimizes a global function of the reaction fluxes with the form of a Hopfield Hamiltonian with hebbian couplings, that is explicitly seen to correspond to the rate of decay of entropy production over time. Guided by this analogy, we show that reaction networks can be formally re-cast as systems of interacting reactions that optimize the use of the available compounds by competing for substrates, akin to agents competing for a limited resource in an optimal allocation problem. As an illustration, we analyze the scenario that emerges in two simple cases: that of toy (random) reaction networks and that of a metabolic network model of the human red blood cell.     

Squalane is in the midplane of the lipid bilayer: implications for its function as a proton permeability barrier

A recently proposed model for proton leakage across biological membranes [Prog. Lipid Res. 40 (2001) 299] suggested that hydrocarbons specifically in the center of the lipid bilayer inhibit proton leaks. Since cellular membranes maintain a proton electrochemical gradient as a principal energy transducer, proton leakage unproductively consumes cellular energy. Hydrocarbons in the bilayer are widespread in membranes that sustain such gradients. The alkaliphiles are unique in that they contain up to 40 mol% isoprenes in their membranes including 10-11 mol% squalene [J. Bacteriol. 168 (1986) 334]. Squalene is a polyisoprene hydrocarbon without polar groups. Localizing hydrocarbons in lipid bilayers has not been trivial. A myriad of physical methods including fluorescence spectroscopy, electron-spin resonance, nuclear magnetic resonance as well as X-ray and neutron diffraction have been used to explore this question with various degrees of success and often contradictory results. Seeking unambiguous evidence for the localization of squalene in membranes or lipid bilayers, we employed neutron diffraction. We incorporated 10 mol% perdeuterated or protonated squalane, an isosteric analogue of squalene, into stacked bilayers of dioleoyl phosphatidyl choline (DOPC) doped with dioleoyl phosphatidyl glycerol (DOPG) to simulate the negative charges found on natural membranes. The neutron diffraction data clearly show that the squalane lies predominantly in the bilayer center, parallel to the plane of the membrane.