PubMed Health⌕ Search

Biomedical subjects

S G Boxer

Publications and source records attributed to S G Boxer.

At least 73 records · Page 4Linked to original sources

Electrostatic interactions in wild-type and mutant recombinant human myoglobins.

Residue Val68 in human myoglobin has been replaced by Asn, Asp, and Glu with site-directed mutagenesis. Purified proteins were characterized by isoelectric focusing and by absorption, CD, and NMR spectroscopy. These studies demonstrated that Mb is able to tolerate substitution of the buried hydrophobic residue Val68 by Asn, Asp, and Glu. In the metaquo derivatives of the Glu and Asp mutants, the negative charge at residue 68 is stabilized by a favorable Coulombic interaction with the heme iron. In the absence of this interaction, as in the metcyano and ferrous deoxy derivatives, the relatively nonpolar protein interior cannot stabilize an isolated buried negative charge, and the carboxylate is either protonated or stabilized via a salt bridge with the nearby distal histidine. Hence in the Asp and Glu mutant proteins, both reduction and cyanide binding are accompanied by proton uptake by the protein. The apoproteins were prepared and reconstituted with the chlorophyll derivative zinc pyrochlorophyllide a. Absorption and fluorescence spectra were quite similar for wild-type and all mutant proteins reconstituted with this derivative. These results do not support the point charge model for the red shifts observed in the spectra of chlorophylls associated with photosynthetic proteins. From the pH dependence of the absorption spectrum of zinc pyrochlorophyllide a in the Glu mutant, the apparent pKa of the buried glutamate residue was estimated to be 8.9. This increase of 4.4 pH units, over the value for Glu in aqueous solution, provides a measure of the polarity of the protein interior.

Codon↗

Multinuclear NMR studies of DNA hairpins. 1. Structure and dynamics of d(CGCGTTGTTCGCG).

The solution structure of the hairpin formed by d(CGCGTTGTTCGCG) has been examined in detail by a wide variety of NMR techniques. The hairpin was characterized by proton NMR to obtain interproton distances and torsion angle information. An energy-minimized model was constructed that is consistent with these data. The hairpin consists of a B-DNA stem of four C-G base pairs and a loop region consisting of five unpaired bases. Three bases in the 5' of the loop are stacked over the 3' end of the stem, and the other two bases in the 3' of the loop are stacked over the 5' end of the stem. The phosphorus NMR spectrum revealed a phosphate in the stem region with an unusual conformation, and two phosphates, P9 and P10, were found to undergo intermediate exchange between conformations. The hairpin was also synthesized with a carbon-13 label in each of the thymidine C6 carbons, and relaxation measurements were performed to determine the extent of internal motions in the loop region. The loop bases are more flexible than the stem bases and exhibit subnanosecond motions with an amplitude corresponding to diffusion in a cone of approximately 30 degrees.

DNA↗

Multinuclear NMR studies of DNA hairpins. 2. Sequence-dependent structural variations.

The solution conformation of three related DNA hairpins, each with five bases in the loop, is investigated by proton and phosphorus 2D NMR methods. The sequences of the three oligomers are d(CGCGTTGTTCGCG), d(CGCGTTTGTCGCG), and d(CTGCTCTTGTTGAGCAG). One pair of hairpins shares the same stem sequence but differs in the loop, and the appearance of an unusual phosphate torsion in the stem is found to depend on the sequence in the loop of the hairpin. The second pair of hairpins shares the same loop region but differs in the stem sequence in that the base pair which closes the loop is a C-G or G-C pair. The pattern of NOEs reveals that the stacking arrangement in the loop region depends on the base pair that closes the stem. These results suggest that hairpin loop conformation and dynamics are sensitive to small changes in the loop and adjacent stem sequences. These findings are discussed in relation to sequence-dependent thermodynamic changes that have been observed in RNA hairpins.

Base Sequence↗

Effects of buried ionizable amino acids on the reduction potential of recombinant myoglobin.

The temperature dependences of the reduction potentials (E degrees') of wild-type human myoglobin (Mb) and three site-directed mutants have been measured by the use of thin-layer spectroelectrochemistry. Residue Val68, which is in van der Waals contact with the heme in Mb, has been replaced by Glu, Asp, and Asn. The changes in E degrees' and the standard entropy (delta S degrees') and enthalpy (delta H degrees') of reduction in the mutant proteins were determined relative to values for wild type; the change in E degrees' at 25 degrees C was about -200 millivolts for the Glu and Asp mutants, and about -80 millivolts for the Asn mutant. At pH 7.0, reduction of Fe(III) to Fe(II) in the Glu and Asp mutants is accompanied by uptake of a proton by the protein. These studies demonstrate that Mb can tolerate substitution of a buried hydrophobic group by potentially charged and polar residues and that such amino acid replacements can lead to substantial changes in the redox thermodynamics of the protein.

Asparagine↗

Synthesis of a thymidine phosphoramidite labelled with 13C at C6: relaxation studies of the loop region in a 13C labelled DNA hairpin.

A thymidine phosphoramidite labelled at C6 with 13C has been synthesized, and incorporated into a synthetic oligonucleotide, d(CGCGT*T*GT*T*CGCG), which adopts a hairpin conformation. NMR relaxation measurements indicate that internal motion may be present in the loop region of the oligonucleotide. The relaxation behavior of a the C6 carbon in a model compound, N,N-1,3 dimethylthymine is examined in detail as a function of magnetic field strength to determine relative contributions of various mechanisms to the relaxation. The relaxation behaviour of the labelled carbons in the oligonucleotide is discussed in relation to these measurements.

Amides↗

Stark effect spectroscopy of Rhodobacter sphaeroides and Rhodopseudomonas viridis reaction centers.

The nature of the initially excited state of the primary electron donor or special pair has been investigated by Stark effect spectroscopy for reaction centers from the photosynthetic bacteria Rhodopseudomonas viridis and Rhodobacter sphaeroides at 77 K. The data provide values for the magnitude of the difference in permanent dipole moment between the ground and excited state, [unk]Deltamu[unk], and the angle [unk] between Deltamu and the transition dipole moment for the electronic transition. [unk]Deltamu[unk] and [unk] for the lowest-energy singlet electronic transition associated with the special pair primary electron donor were found to be very similar for the two species. [unk]Deltamu[unk] for this transition is substantially larger than for the Q(y) transitions of the monomeric pigments in the reaction center or for pure monomeric bacteriochlorophylls, for which Stark data are also reported. We conclude that the excited state of the special pair has substantial charge-transfer character, and we suggest that charge separation in bacterial photosynthesis is initiated immediately upon photoexcitation of the special pair. Data for Rhodobacter sphaeroides between 340 and 1340 nm are presented and discussed in the context of the detection of charge-transfer states by Stark effect spectroscopy.

Journal Article↗

Cloning, expression in Escherichia coli, and reconstitution of human myoglobin.

A full-length cDNA clone for human myoglobin has been isolated from a human skeletal muscle cDNA library. The clone as isolated has a cDNA insert approximately one kilobase long and has 5' and 3' untranslated regions of approximately 80 and 530 base pairs, respectively. The sequence of the translated region corresponds exactly to that predicted for human myoglobin. The cDNA was expressed in high yield in Escherichia coli as a fusion protein consisting of the first 31 amino acids of the phage lambda cII gene, the tetrapeptide Ile-Glu-Gly-Arg, and the myoglobin sequence by following the approach of Nagai and Thogersen [Nagai, K. & Thogersen, M. C. (1984) Nature (London) 309, 810-812]. The fusion product was isolated, reconstituted with heme, cleaved with trypsin, and purified to generate a protein whose properties are indistinguishable from those for authentic human myoglobin. Myoglobin can be readily prepared on a gram scale by using these methods.

Bacterial Proteins↗

Effect of magnetic fields on the triplet state lifetime in photosynthetic reaction centers: Evidence for thermal repopulation of the initial radical pair.

The lifetime of the molecular triplet state formed by recombination of the radical ion pair in quinonedepleted bacterial photosynthetic reaction centers is found to depend on applied magnetic field strength. It is suggested that this magnetic field effect results from thermally activated repopulation of the same radical ion pair that generates the triplet. Consistent with this hypothesis, the magnetic field effect on the triplet lifetime disappears at low temperature where the triplet state decays exclusively by ordinary intersystem crossing. This activated pathway for the decay of the triplet state can explain the strong temperature dependence of the triplet decay rate. A detailed theoretical treatment of the problem within a set of physically reasonable assumptions relates the observed temperature dependence of the triplet decay rate to the energy gap between the radical ion pair intermediate and the triplet state. This energy gap is estimated to be about 950 cm(-1) (0.12 eV). Combined with an estimate of the energy of the donor excited state, we obtain an energy gap between the excited singlet state of the donor and the radical ion pair of 2,250 cm(-1) (0.28 eV).

Journal Article↗

Chemically induced dynamic nuclear polarization studies of yeast tRNAPhe.

Chemically induced dynamic nuclear polarization (CIDNP) has been observed from yeast tRNAPhe following reaction with photoexcited riboflavin. At 20 degrees C, several resonances of tRNA in the native form show polarization; previous work predicts that only guanosine and its derivatives in single-stranded regions are likely to become polarized [ McCord , E.F., Morden , K. M., Pardi , A., Tinoco , I., Jr., & Boxer, S. G. (1984) Biochemistry (preceding paper in this issue)]. The methyl protons of m22G -26 show strong negative spin polarization, indicating that this residue is accessible. The solvent accessibility of this residue has not been previously demonstrated. In addition, two positively polarized aromatic resonances are observed, which are likely due to two or more G(H8) protons, including those of G-20, m22G -26, and/or Gm-34. For temperatures below 50 degrees C, a negatively polarized signal in the aromatic region is shown to arise from cross relaxation with the methyl group protons of m22G -26. This indicates the proximity of an aromatic proton, probably H2 of A-44, to the methyl groups of m22G -26. At higher temperatures, the CIDNP spectra show polarization of several additional G resonances, including those of m2G -10. These changes in the CIDNP spectra reflect melting of the tertiary and secondary structure of the tRNA. This work is the first use of CIDNP to study a large nucleic acid molecule and exemplifies the value of this technique in probing single-stranded and solvent-accessible regions of tRNA.

Chemical Phenomena↗

Excitation transport and trapping in a synthetic chlorophyllide substituted hemoglobin: orientation of the chlorophyll S1 transition dipole.

Excitation transport in synthetic zinc chlorophyllide substituted hemoglobin has been observed by pico -second time-resolved fluorescence depolarization experiments. In this hybrid molecular system, two zinc chlorophyllide molecules are substituted into the beta-chains of hemoglobin, while deoxy hemes remain in the alpha-chains. The rate of excitation transfer between the two chlorophyllides is analyzed in terms of the distance and orientation dependences predicted by the F orster dipole-dipole theory. In this analysis, the beta-beta interchromophore geometry is assumed to be that of the deoxyhemoglobin crystal structure. When combined with steady-state fluorescence depolarization data of the complementary hybrid containing zinc chlorophyllide in the alpha-chains, these experiments provide the necessary information to determine the orientation of the S1 transition dipole moment in the zinc chlorophyllide molecule. We also find that the fluorescence lifetime of the zinc chlorophyllide is 1.42 ns when the heme is in the deoxy state but 3.75 ns when the heme is ligated to carbon monoxide. This is explained by irreversible excitation transfer from the S1 state of the zinc chlorophyllide to the lower energy excited states present in deoxy heme.

Chlorophyll↗

Chlorophyllide-substituted hemoglobin tetramers and hybrids: preparation, characterization, and energy transfer.

Three chlorophyllide-substituted human hemoglobin (Hb) complexes have been prepared: the tetrameric complex in which zinc pyrochlorophyllide alpha (ZnPChl alpha) is substituted for all four hemes and the two complementary hybrids in which ZnPChl alpha is substituted for heme in either the alpha- or beta-chains, while heme remains in the other chains. In each of these complexes, intramolecular Chl-Chl singlet energy transfer occurs. A variety of probes demonstrate that ZnPChl alpha-deoxyheme hybrids and the ZnPChl alpha-Hb complexes consistently exhibit properties associated with the well-known T-state tertiary and quaternary structure of deoxyHb itself. Using the known crystal structure of human deoxyHb, we have analyzed the steady-state fluorescence anisotropy of these complexes within the framework of the Förster energy-transfer theory. The result is the determination of the orientation of the Qy transition dipole moment of ZnPChl alpha. Nuclear magnetic resonance data for the hybrids offer insight into specific tertiary structural changes in the heme pocket surrounding the diamagnetic ZnPChl alpha, which accompany changes in the ligation state of the heme on the opposite chain.

Chlorophyll↗

Anisotropic magnetic interactions in the primary radical ion-pair of photosynthetic reaction centers.

The quantum yield of triplets formed by ion-pair recombination in quinone-depleted photosynthetic reaction centers is found to depend on their orientation in a magnetic field. This new effect is expected to be a general property of radical pair reactions in the solid state. For 0 < H < 1,000 G, the quantum yield anisotropy is caused by anisotropic electron dipole-electron dipole or nuclear hyperfine interactions, or both. For high fields it is dominated by the anisotropy of the difference g-tensor in the radical ion-pair. The magnitude and sign of the contribution of each interaction depend not only on the values of the principal components of each anisotropic tensor but also on the geometric relationship of the principal axes of each tensor to the transition dipole moment used to detect the yield. A detailed formalism is presented relating these quantities to the observed yield anisotropy. The expected magnitude of each anisotropic parameter is discussed. It is demonstrated that the field dependence of the yield anisotropy is consistent with these values for certain reaction center geometries.

Journal Article↗

Oriented properties of the chlorophylls: Electronic absorption spectroscopy of orthorhombic pyrochlorophyllide a-apomyoglobin single crystals.

The orientations of the transition dipole moments in chlorophyll (Chl) are among the most useful spectroscopic properties for determining macromolecular architecture in photosynthetic complexes; however, the relationships between these orientations and the Chl molecular geometry are unknown. In order to solve this problem, we have prepared single crystals of the synthetic 1:1 complex between pyrochlorophyllide a and apomyoglobin. The protein crystallizes readily in the orthorhombic (B) form, space group P2(1)2(1)2(1), and the unit cell dimensions are determined to be within 0.5% of those for native MetMb crystals of the same type. These green crystals are highly dichroic, and the strong absorption along the crystallographic a axis in the Q(y) band is red-shifted by about 9 nm, relative to the corresponding feature in a solution of the protein. Although the crystal structure for native Mb in this space group has not been determined, the direction cosines of the heme normal relative to the crystal axes have been measured. By using these values, an appropriate trigonometric analysis, and the measured polarized single-crystal spectra, the orientation of the Chl transition dipole moment for the Q(y) transition can be specified relative to the crystal axes. With the completion of the protein crystal structure, this result will lead directly to the orientations of the optical transition dipole moments relative to the molecular geometry. The effects of vibronic coupling and the protein environment on the absorption properties of Chl are discussed in detail.

Journal Article↗

Solution properties of synthetic chlorophyllide--and bacteriochlorophyllide--apomyoglobin complexes.

Well-defined 1:1 complexes have been formed between apomyoglobin (apoMb) and a number of chlorophyllide derivatives. The chlorophyllides substitute for heme in the pocket of myoglobin. These include magnesium chlorophyllide a, magnesium and zinc pyrochlorophyllide a, zinc pyrochlorophyllide b, zinc pyrochlorophyllide d, zinc pyromesochlorophyllide a, zinc 2-acetyl-2-devinylpyrochlorophyllide a, zinc protopyrochlorophyllide a, and zinc bacteriopyrochlorophyllide a. The effects of the protein on the electronic absorption, circular dichroism (CD), magnetic circular dichroism, and triplet state electron spin resonance spectra and fluorescence lifetimes in solution are compared with appropriate models in organic solvents. With the exception of the CD spectra, the protein causes shifts and intensity changes which are within the range observed for solvent effects. The CD spectra change substantially: the signs of several transitions are entirely reversed in the chlorins, and 3-6-fold intensity increases are observed with zinc bacteriochlorophyllide a. High-field 1H NMR spectra of ring current shifted Val-E11 methyl protons for the series porphyrin-, chlorin-, and bacteriochlorin-apoMb are used to establish the probable absolute orientation of the chromophore in the heme pocket. Doubled peaks in the NMR spectra of certain complexes are shown to arise from interconvertible species. The temperature dependence of the peak intensities and saturation transfer studies show that the species giving rise to the doubled peaks exchange on the time scale of about 1-60 s. Arguments are presented against inversion of the macrocycle in the heme pocket by either an inter- or an intramolecular mechanism as the origin of doubled peaks, and simple two-site exchange is ruled out by the NMR data. We suggest that the data are consistent with the idea that at least two slowly interconverting conformational substrates of the protein are populated, depending sensitively on small changes in rings I and II of the macrocycle and temperature.

Apoproteins↗

Laser chemically induced dynamic nuclear polarization study of the reaction between photoexcited flavins and tryptophan derivatives at 360 MHz.

Chemically induced dynamic nuclear polarization (CIDNP) is generated when tryptophan (Trp), its derivatives, or Trp-containing peptides react with photoexcited flavins in a 360-MHz NMR spectrometer. In contrast to tyrosine (Tyr), we find that the nuclear polarization of Trp originates in an electron-transfer reaction. By use of a series of Trp derivatives, the unpaired spin-density distribution of the Trp radical cation and the ground-state NMR spectrum of Trp are analyzed in detail. The signs and the relative magnitudes of the proton isotropic hyperfine coupling constants for each position around the indole ring in the radical cation deduced from these measurements are the following: position 3 greater than 2 approximately 4 approximately 6 greater than 1 greater than 5 greater than 7, with positions 1, 2, 3, 4, and 6 positive, 5 negative, and 7 essentially zero. This result is inconsistent with most available calculations of the unpaired spin-density distribution but is compatible with the pattern of electrophilic aromatic substitution. The origin of this discrepancy is discussed in detail. Possible mechanistic complications in the reaction leading to CIDNP are discussed. The laser CIDNP spectra of the Trp-rich peptides gramicidins A and B are presented as examples of the resolution enhancement obtained with this technique.

Energy Transfer↗

Chromophore organization in photosynthetic reaction centers: High-resolution magnetophotoselection.

The electron spin resonance spectrum of the triplet excited state of Rhodopseudomonas spheroides R-26 reaction centers has been studied after excitation with the polarized narrow-bandwidth output of a tunable dye laser from 520 to 670 nm. A theory is developed relating experimental observables to the angles between the electronic transition dipole moment of the excited chromophore and the principle magnetic axis system of the triplet state of the dimeric trap. Data is presented which demonstrates that the treatment is correct and useful, and angles are obtained for the Q(x) transitions of bacteriopheophytin. High-resolution magnetophotoselection data in the region of the bacteriochlorophyll Q(x) transitions can be combined with polarized photobleaching experiments to provide direct information on the structure of dimeric trap.

Journal Article↗