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At least 217 records · Page 12Linked to original sources
PubMed2003

Conformational dynamics of the Na+/K+-ATPase probed by voltage clamp fluorometry.

The method of voltage clamp fluorometry combined with site-directed fluorescence labeling was used to detect local protein motions of the fully active Na(+)K(+)-ATPase in real time under physiological conditions. Because helix M5 extends from the cytoplasmic site of ATP hydrolysis into the cation binding region, we chose the extracellular M5-M6 loop of the sheep alpha(1)-subunit for the insertion of cysteine residues to identify reporter positions for conformational rearrangements during the catalytic cycle. After expression of the single cysteine mutants in Xenopus oocytes and covalent attachment of tetramethylrhodamine-6-maleimide, only mutant N790C reported molecular rearrangements of the M5-M6 loop by showing large, ouabain-sensitive fluorescence changes ( approximately 5%) on addition of extracellular K(+). When the enzyme was subjected to voltage jumps under Na(+)Na(+)-exchange conditions, we observed fluorescence changes that directly correlated to transient charge movements originating from the E(1)P-E(2)P transition of the transport cycle. The voltage jump-induced fluorescence changes and transient currents were abolished after replacement of Na(+) by tetraethylammonium or on addition of ouabain, showing that conformational flexibility is impaired under these conditions. Voltage-dependent fluorescence changes could also be observed in the presence of subsaturating K(+) concentrations. This allowed to monitor the time course of voltage-dependent relaxations into a new stationary distribution of states under turnover conditions, showing the acceleration of relaxation kinetics with increasing K(+) concentrations. As a result, the stationary distribution between E(1) and E(2) states and voltage-dependent relaxation times can be determined at any time and membrane potential under Na(+)Na(+) exchange as well as Na(+)K(+) turnover conditions.

Adenosine Triphosphate↗
PubMed2000

Formation, structure and conformational dynamics of highly substituted diphenylcarbonates

The symmetrical carbonates 5-8 were prepared from ethyl 4-hydroxybenzoates with aryl-, 4-(arylethynyl)-phenyl-, arylethynyl- or arylbutadiynyl-substituents in the 3- and 5-positions, by reaction with triphosgene. The choice of base (pyridine, DMAP, NaH) had a strong influence on the conversion: For the synthesis of the carbonates 5 and 6, it was sufficient to use pyridine as the base. However, for the synthesis of the carbonates 7 and 8, NaH had to be used instead. Single-crystal X-ray structure analysis of these carbonates revealed that the substituents point towards the corners of a distorted tetrahedron with the carbonate group sitting in the middle of the tetrahedron and the two angular phenolic building blocks intersecting with an angle of 51-71 degrees. In solution at room temperature, all four substituents are magnetically equivalent as a consequence of conformational flexibility. The two enantiomeric conformers of carbonate 5a interconvert rapidly, probably via a perfect trans conformation with the plane of the Aralpha perpendicular to the carbonate plane. In the case of carbonates 6-8 this process is inhibited by unfavourable interaction of the long substituents at the benzoate moiety. The dynamic process, which has an energy barrier of 8-10 kcalmol(-1), is described in a simplified manner as a continuous rotation of the angular building blocks around the carbonate unit with the C(aryl)-O bonds as the axes of rotation.

Journal Article↗
PubMed1998

Introduction of a tryptophan reporter group into the ATP binding motif of the Escherichia coli UvrB protein for the study of nucleotide binding and conformational dynamics.

The DNA-dependent ATPase activity of UvrB is required to support preincision steps in nucleotide excision repair in Escherichia coli. This activity is, however, cryptic. Elicited in nucleotide excision repair by association with the UvrA protein, it may also be unmasked by a specific proteolysis eliminating the C-terminal domain of UvrB (generating UvrB*). We introduced fluorescent reporter groups (tryptophan replacing Phe47 or Asn51) into the ATP binding motif of UvrB, without significant alteration of behavior, to study both nucleotide binding and those conformational changes expected to be essential to function. The inserted tryptophans occupy moderately hydrophobic, although potentially heterogeneous, environments as evidenced by fluorescence emission and time-resolved decay characteristics, yet are accessible to the diffusible quencher acrylamide. Activation, via specific proteolysis, is accompanied by conformational change at the ATP binding site, with multiple changes in emission spectra and a greater shielding of the tryptophans from diffusible quencher. Titration of tryptophan fluorescence with ATP has revealed that, although catalytically incompetent, UvrB can bind ATP and bind with an affinity equal to that of the active UvrB* form (Kd of approximately 1 mM). The ATP binding site of UvrB is therefore functional and accessible, suggesting that conformational change either brings amino acid residues into proper alignment for catalysis and/or enables response to effector DNA.

Adenosine Triphosphatases↗
PubMed2005

Conformational dynamics of the isoalloxazine in substrate-free p-hydroxybenzoate hydroxylase: single-molecule studies.

p-Hydroxybenzoate hydroxylase (PHBH) is a homodimeric enzyme in which each subunit noncovalently binds one molecule of FAD in the active site. PHBH is a model system for how flavoenzymes regulate reactions with oxygen. We report single-molecule fluorescence studies of PHBH in the absence of substrate that provide data consistent with the hypothesis that a critical step in substrate binding is the movement of the isoalloxazine between an "in" conformation and a more exposed or "open" conformation. The isoalloxazine is observed to move between these conformations in the absence of substrate. Studies with the Y222A mutant form of PHBH suggest that the exposed conformation is fluorescent while the in-conformation is quenched. Finally, we note that many of the single-molecule-fluorescence trajectories reveal a conformational heterogeneity, with populations of the enzyme characterized by either fast or slow switching between the in- and open-conformations. Our data also allow us to hypothesize a model in which one flavin in the dimer inhibits the motion of the other.

4-Hydroxybenzoate-3-Monooxygenase↗
PubMed2002

Conformational dynamics of photoexcited conjugated molecules.

Time-dependent photoexcitation and optical spectroscopy of pi-conjugated molecules is described using a new method for the simulation of excited state molecular dynamics in extended molecular systems with sizes up to hundreds of atoms. Applications are made to poly(p-phenylene vinylene) oligomers. Our analysis shows self-trapping of excitations on about six repeat units in the course of photoexcitation relaxation, identifies specific slow (torsion) and fast (bond-stretch) nuclear motions strongly coupled to the electronic degrees of freedom, and predicts spectroscopic signatures of molecular conformations.

Journal Article↗
PubMed1991

Conformational dynamics of unfolded peptides as a function of chain length: a frequency domain fluorescence approach.

The fluorescence emission decays of single-tryptophan-containing peptides of different chain lengths in their unfolded state were investigated in the frequency domain. The data were analyzed using different functions, i.e., exponential fit and probability-density functions of different shape. We found that unimodal Lorentzian distributions best describe the fluorescence decays. This finding agrees with the point of view, now broadly accepted, that rapid motions exist in polypeptides. As a consequence of this flexibility, a large variety of conformations, with an unequal perturbation of tryptophan in its excited state, is generated. The lifetime distribution center was independent of the length of the polypeptide chain but strongly related to the nature of the amino acid residues located in the proximity of the tryptophan in the primary structure. The full width at half maximum, W, of the lifetime distribution was found to be related to the length of unfolded polypeptide by the empirical logarithmic relationship W = 0.83 log n, where n indicates the number of residues. For short peptides, a single lifetime or a narrow range of lifetimes is observed because of the fast relaxation of the tryptophanyl environment. On peptide lengthening, the spectrum of conformations, which the peptide can assume, increases; this causes a complex fluorescence decay represented by a lifetime distribution. For long polypeptide chains, the motions of the regions far from tryptophan do not significantly perturb the chromophore environment.

Amino Acid Sequence↗
PubMed2004

Effect of the Met344His mutation on the conformational dynamics of bovine beta-1,4-galactosyltransferase: crystal structure of the Met344His mutant in complex with chitobiose.

Beta-1,4-galactosyltransferase (beta4Gal-T1) in the presence of manganese ion transfers galactose from UDP-galactose (UDP-Gal) to N-acetylglucosamine (GlcNAc) that is either free or linked to an oligosaccharide. Crystallographic studies on bovine beta4Gal-T1 have shown that the primary metal binding site is located in the hinge region of a long flexible loop, which upon Mn(2+) and UDP-Gal binding changes from an open to a closed conformation. This conformational change creates an oligosaccharide binding site in the enzyme. Neither UDP nor UDP analogues efficiently induce these conformational changes in the wild-type enzyme, thereby restricting the structural analysis of the acceptor binding site. The binding of Mn(2+) involves an uncommon coordination to the Sdelta atom of Met344; when it is mutated to His, the mutant M344H, in the presence of Mn(2+) and UDP-hexanolamine, readily changes to a closed conformation, facilitating the structural analysis of the enzyme bound with an oligosaccharide acceptor. Although the mutant M344H loses 98% of its Mn(2+)-dependent activity, it exhibits 25% of its activity in the presence of Mg(2+). The crystal structures of M344H-Gal-T1 in complex with either UDP-Gal.Mn(2+) or UDP-Gal.Mg(2+), determined at 2.3 A resolution, show that the mutant enzyme in these complexes is in a closed conformation, and the coordination stereochemistry of Mg(2+) is quite similar to that of Mn(2+). Although either Mn(2+) or Mg(2+), together with UDP-Gal, binds and changes the conformation of the M344H mutant to the closed one, it is the Mg(2+) complex that engages efficiently in catalyses. Thus, this property enabled us to crystallize the M344H mutant for the first time with the acceptor substrate chitobiose in the presence of UDP-hexanolamine and Mn(2+). The crystal structure determined at 2.3 A resolution reveals that the GlcNAc residue at the nonreducing end of chitobiose makes extensive hydrophobic interactions with the highly conserved Tyr286 residue.

Acetylglucosamine↗
PubMed1988

Conformational dynamics of cytochalasin B in solution as detected by 13C and 1H NMR relaxation rates.

13C and 1H NMR spin-lattice relaxation rates have been measured for cytochalasin B in [2H]6DMSO. Motional features have been interpreted in terms of nearly isotropic reorientation of the whole molecule with few additional internal motions. The 'isotropic' reorientational correlation time was evaluated at 0.21 ns at room temperature. By using selective and double-selective excitation techniques, relevant cross-relaxation terms have been obtained wherefrom proton-proton distances have been calculated. A Dreiding model of the 'preferred' conformation in solution has been built, yielding evidence of a strong similarity between solution and solid state structures of cytochalasin B.

Carbon Isotopes↗
PubMed2003

Protein conformational dynamics probed by single-molecule electron transfer.

Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over time. We could then determine the potential of mean force between the flavin and the tyrosine, and a correlation analysis revealed conformational fluctuation at multiple time scales spanning from hundreds of microseconds to seconds. This phenomenon suggests the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.

Amino Acid Substitution↗
PubMed1995

DNA conformational dynamics in polymer solutions above and below the entanglement limit.

Video microscopy of nucleic acids (DNA) undergoing electrophoresis in hydroxyethyl cellulose (HEC) sieving buffers demonstrates previously unobserved shape-changing interactions between DNA and HEC molecules. We provide the first visual demonstration of entanglement between DNA and one or several discrete HEC molecules, which has been postulated to occur in ultradilute polymer solutions. Typically, nucleic acids appear to become entangled with HEC at a single region only, in both dilute and fully entangled HEC solutions. Fluctuations of the center of mass velocity of a DNA molecule and its correlation with conformation are revealed from analyses of the image data. These observations account for the success of recently reported rapid, high-resolution dc and pulsed-field capillary electrophoretic separations of nucleic acids in ultradilute hydroxyethyl cellulose solutions and hydroxyethyl cellulose/poly(ethylene oxide) solutions.

Cellulose↗
PubMed1992

Conformational dynamics and intersubunit energy transfer in wild-type and mutant lipoamide dehydrogenase from Azotobacter vinelandii. A multidimensional time-resolved polarized fluorescence study.

Time-resolved fluorescence and fluorescence anisotropy data surfaces of flavin adenine dinucleotide bound to lipoamide dehydrogenase from Azotobacter vinelandii in 80% glycerol have been obtained by variation of excitation energy and temperature between 203 and 303 K. The fluorescence kinetics of a deletion mutant lacking 14 COOH-terminal amino acids were compared with the wild-type enzyme to study a possible interaction of the COOH-terminal tail with the active site of the enzyme. The flavin adenine dinucleotide fluorescence in both proteins exhibits a bimodal lifetime distribution as recovered by the maximum entropy method of data analysis. The difference in standard enthalpy and entropy of associated conformational substates was retrieved from the fractional contributions of the two lifetime classes. Activation energies of thermal quenching were obtained that confirm that the isoalloxazines in the deletion mutant are solvent accessible in contrast to the wild-type enzyme. Red-edge spectroscopy in conjunction with variation of temperature provides the necessary experimental axes to interpret the fluorescence depolarization in terms of intersubunit energy transfer rather than reorientational dynamics of the flavins. The results can be explained by a compartmental model that describes the anisotropy decay of a binary, inhomogeneously broadened, homoenergy transfer system. By using this model in a global analysis of the fluorescence anisotropy decay surface, the distance between and relative orientation of the two isoalloxazine rings are elucidated. For the wild-type enzyme, this geometrical information is in agreement with crystallographic data of the A. vinelandii enzyme, whereas the mutual orientation of the subunits in the deletion mutant is slightly altered. In addition, the ambiguity in the direction of the emission transition moment in the isoalloxazine ring is solved. The anisotropy decay parameters also provide information on electronic and dipolar relaxational properties of the flavin active site. The local environment of the prosthetic groups in the deletion mutant of the A. vinelandii enzyme is highly inhomogeneous, and a transition from slow to rapid dipolar relaxation is observed over the measured temperature range. In the highly homogeneous active site of the wild-type enzyme, dipolar relaxation is slowed down beyond the time scale of fluorescence emission at any temperature studied. Our results are in favor of a COOH-terminal polypeptide interacting with the active site, thereby shielding the isoalloxazines from the solvent. This biological system forms a very appropriate tool to test the validity of photophysical models describing homoenergy transfer.

Azotobacter vinelandii↗
PubMed2005

Internucleotide movements during formation of 16 S rRNA-rRNA photocrosslinks and their connection to the 30 S subunit conformational dynamics.

UV light-induced RNA photocrosslinks are formed at a limited number of specific sites in the Escherichia coli and in other eubacterial 16 S rRNAs. To determine if unusually favorable internucleotide geometries could explain the restricted crosslinking patterns, parameters describing the internucleotide geometries were calculated from the Thermus thermophilus 30 S subunit X-ray structure and compared to crosslinking frequencies. Significant structural adjustments between the nucleotide pairs usually are needed for crosslinking. Correlations between the crosslinking frequencies and the geometrical parameters indicate that nucleotide pairs closer to the orientation needed for photoreaction have higher crosslinking frequencies. These data are consistent with transient conformational changes during crosslink formation in which the arrangements needed for photochemical reaction are attained during the electronic excitation times. The average structural rearrangement for UVA-4-thiouridine (s4U)-induced crosslinking is larger than that for UVB or UVC-induced crosslinking; this is associated with the longer excitation time for s4U and is also consistent with transient conformational changes. The geometrical parameters do not completely predict the crosslinking frequencies, implicating other aspects of the tertiary structure or conformational flexibility in determining the frequencies and the locations of the crosslinking sites. The majority of the UVB/C and UVA-s4U-induced crosslinks are located in four regions in the 30 S subunit, within or at the ends of RNA helix 34, in the tRNA P-site, in the distal end of helix 28 and in the helix 19/helix 27 region. These regions are implicated in different aspects of tRNA accommodation, translocation and in the termination reaction. These results show that photocrosslinking is an indicator for sites where there is internucleotide conformational flexibility and these sites are largely restricted to parts of the 30 S subunit associated with ribosome function.

Base Pairing↗
PubMed1995

Solution conformational dynamics of the C-terminal residues in endothelin-1 and some analogues: a time-resolved fluorescence study.

The rotational relaxation times of the single tryptophan residues in endothelin-1, [Ala1,3,11,15]endothelin-1, human pro-endothelin-1, the linear hexapeptide Ac-His-Leu-Asp-Ile-Ile-Trp which corresponds to the C-terminal residues 16-21 in endothelin-1, the cyclic pentapeptide BQ123, and several di- and tri-peptides possessing C-terminal tryptophan residues have been determined from time-resolved fluorescence anisotropy decays obtained by phase/modulation techniques. Fluorescence lifetime distribution widths have also been examined as predictors of conformational heterogeneity/restriction. A significant contribution from a slow rotational component supports either the persistence, on the nano-second timescale at least, of a non-flexible alpha-helical structure for the C-terminal tail residues of endothelin-1 in water as solvent, as seen in the X-ray crystallographic structure, or the interaction of the C-terminal tail residues 16-21 with the constrained disulfide-bridged core residues 1-15. This slow rotational contribution is less evident in the linear, acyclic tetraalanine analogue but greatly increased in pro-endothelin-1. In BQ123 the fluorescence characteristics support the occurrence of a dominant rotameric form involving the indole sidechain of the D-tryptophan residue (C alpha-C beta torsion angle chi 1 of 60 degrees, as previously determined by NMR.

Amino Acid Sequence↗
PubMed1994

Conformational dynamics of bovine Cu, Zn superoxide dismutase revealed by time-resolved fluorescence spectroscopy of the single tyrosine residue.

The structural dynamics of bovine erythrocyte Cu, Zn superoxide dismutase (BSOD) was studied by time-resolved fluorescence spectroscopy. BSOD is a homodimer containing a single tyrosine residue (and no tryptophan) per subunit. Frequency-domain fluorometry revealed a heterogeneous fluorescence decay that could be described with a Lorentzian distribution of lifetimes. The lifetime distribution parameters (center and width) were markedly dependent on temperature. The distribution center (average lifetime) displayed Arrhenius behavior with an Ea of 4.2 kcal/mol, in contrast with an Ea of 7.4 kcal/mol for the single-exponential decay of L-tyrosine. This indicated that thermal quenching of tyrosine emission was not solely responsible for the effect of temperature on the lifetimes of BSOD. The distribution width was broad (1 ns at 8 degrees C) and decreased significantly at higher temperatures. Furthermore, the width of the lifetime distribution increased in parallel to increasing viscosity of the medium. The combined effects of temperature and viscosity on the fluorescence decay suggest the existence of multiple conformational substrates in BSOD that interconvert during the excited-state lifetime. Denaturation of BSOD by guanidine hydrochloride produced an increase in the lifetime distribution width, indicating a larger number of conformations probed by the tyrosine residue in the denatured state. The rotational mobility of the tyrosine in BSOD was also investigated. Analysis of fluorescence anisotropy decay data enabled resolution of two rotational correlation times. One correlation time corresponded to a fast (picosecond) rotation that contributed 62% of the anisotropy decay and likely reported local mobility of the tyrosine ring. The longer correlation time was 50% of the expected value for rotation of the whole (dimeric) BSOD molecule and appeared to reflect segmental motions in the protein in addition to overall tumbling. Comparison between rotational correlation times and fluorescence lifetimes of BSOD indicates that the heterogeneity in lifetimes does not arise from mobility of the tyrosine per se, but rather from dynamics of the protein matrix surrounding this residue which affect its fluorescence decay.

Animals↗
PubMed1991

Conformational dynamics of the formyl peptide receptor: a prototype for studies of receptor dynamics and binding pocket structure.

We have used spectrofluorometric and flow cytometric techniques to examine the interactions of formyl peptide ligands (L) with their cell surface receptors (R). Kinetic studies suggest that L binds to R at a diffusion limited rate and that R undergoes rapid transitions involving three states (LR, LRG, the ternary complex of L and R with the G protein, and a desensitized receptor "LRX" which forms within seconds) prior to internalization. A spectroscopic analysis of the interaction between L and R show that the binding pocket of R is large enough to contain no more than 6 amino acids and that a fluorescein-labelled pentapeptide is quenched upon binding to R. We hypothesize that histidine 90 (putatively located in the extracellular loop connecting the second and third transmembrane domains) protonates L and quenches the probe. New technology will extend the analysis of structure and dynamics to low affinity peptide receptors of living biological systems. Such technology will have implications in the design of peptidomimetic ligand and drug molecules.

Animals↗