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PubMed2001

Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics.

A template-assisted conformational change of the cellular prion protein (PrP(C)) from a predominantly helical structure to an amyloid-type structure with a higher proportion of beta-sheet is thought to be the causative factor in prion diseases. Since flexibility of the polypeptide is likely to contribute to the ability of PrP(C) to undergo the conformational change that leads to the infective state, we have undertaken a comprehensive examination of the dynamics of two recombinant Syrian hamster PrP fragments, PrP(29-231) and PrP(90-231), using (15)N NMR relaxation measurements. The molecular motions of these PrP fragments have been studied in solution using (15)N longitudinal (T(1)) and transverse relaxation (T(2)) measurements as well as [(1)H]-(15)N nuclear Overhauser effects (NOE). These data have been analyzed using both reduced spectral density mapping and the Lipari-Szabo model free formalism. The relaxation properties of the common regions of PrP(29-231) and PrP(90-231) are very similar; both have a relatively inflexible globular domain (residues 128-227) with a highly flexible and largely unstructured N-terminal domain. Residues 29-89 of PrP(29-231), which include the copper-binding octarepeat sequences, are also highly flexible. Analysis of the spectral densities at each residue indicates that even within the structured core of PrP(C), a markedly diverse range of motions is observed, consistent with the inherent plasticity of the protein. The central portions of helices B and C form a relatively rigid core, which is stabilized by the presence of an interhelix disulfide bond. Of the remainder of the globular domain, the parts that are not in direct contact with the rigid region, including helix A, are more flexible. Most significantly, slow conformational fluctuations on a millisecond to microsecond time scale are observed for the small beta-sheet. These results are consistent with the hypothesis that the infectious, scrapie form of the protein PrP(Sc) could contain a helical core consisting of helices B and C, similar in structure to the cellular form PrP(C). Our results indicate that residues 90-140, which are required for prion infectivity, are relatively flexible in PrP(C), consistent with a lowered thermodynamic barrier to a template-assisted conformational change to the infectious beta-sheet-rich scrapie isoform.

Animals↗
PubMed1987

Local structural features around the C-terminal segment of Streptomyces subtilisin inhibitor studied by carbonyl carbon nuclear magnetic resonances three phenylalanyl residues.

The carbonyl carbon NMR signals of the Phe residues in Streptomyces subtilisin inhibitor (SSI) were selectively observed for [F]SSI, in which all phenylalanines were uniformly labeled with [1-13C]Phe. The three enhanced resonances in the spectrum of [F]SSI were unambiguously assigned to the specific sites in the amino acid sequence by means of 15N,13C double-labeling techniques. Namely, the resonances at 174.9 and 172.6 ppm (in D2O, pH 7.3, 50 degrees C) showed the satellite peaks due to 13C-15N spin coupling in the spectra of [F,GS]SSI and [F,A]SSI, in which Ser/Gly and Ala residues were labeled with [15N]Gly/Ser and [15N]Ala, respectively, together with [1-13C]Phe. The carbonyl groups of Phe-97 and Phe-111 are involved in peptide bonds with the amino nitrogens of Ser-98 and Ala-112, respectively. These results clearly indicate that the signals at 174.5 and 172.6 ppm are due to Phe-97 and Phe-111, respectively. The signal at the lowest field (177.1 ppm) was thus assigned to the carboxyl carbon of the C-terminal Phe-113. The lifetimes of the amide hydrogens of the three Phe residues and their C-terminal-side neighbors (Ser-98 and Ala-112) were investigated by using the effect of deuterium-hydrogen exchange of amide on the line shapes (DEALS) for the Phe carbonyl carbon resonances. In this method, the NMR spectra of [F]SSI dissolved in 50% D2O (pH 7.3) were measured at various temperatures, and the line shape changes caused by deuteriation isotope shifts were analyzed.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1990

Coupling between local structure and global stability of a protein: mutants of staphylococcal nuclease.

Staphylococcal nuclease exists in solution as a mixture of two folded (N and N') and two unfolded (U and U*) forms. Earlier workers [Evans et al. (1989) Biochemistry 28, 362] have proposed that the N'/N and U/U* structural differences involve cis/trans isomerization about the Lys116-Pro117 peptide bond with N and U cis and N' and U* trans. The present results show that residue changes throughout the nuclease structure have large effects on the distribution of the N and N'forms. The N'/N ratios at 313 K for nuclease H124L (N'/N = 0.07) and nuclease G79S (N'/N = 12) differ by 2 orders of magnitude. Thermodynamic parameters for equilibria linking the two folded and two unfolded substates were evaluated for seven mutants of nuclease which were found by kinetic assays to have similar enzymatic activities but by NMR spectroscopy to have a wide dispersion of thermal stabilities. Our results indicate that mutational perturbations of the N'/N equilibrium in folded nuclease (delta G for the N in equilibrium N' reaction) are strongly coupled to changes in the stability of the N form (delta G for the N in equilibrium U reaction), but much less so to the stability of the N' form (delta G for the N' in equilibrium U* reaction).

Amino Acid Sequence↗
PubMed2004

Successful design and synthesis of a polarity-triggered beta-->alpha conformational switch using the side chain interaction index (SCII) as a measure of local structural stability.

Certain sequences within proteins have the ability to undergo an abrupt cooperative conformational switch from beta-strand to helix in response to decreasing polarity of the environment. This behavior was first observed at the CD4 binding site of the envelope glycoprotein gp120 of HIV-1, but evidence has accumulated that polarity-driven beta --> alpha switches may be widespread, serving both to facilitate binding on protein/membrane or protein/protein contact and to signal that docking has occurred. The characteristics identified so far that distinguish switch sequences (a reverse turn at the N-terminus that acts as a helix initiation site, a conserved tryptophan residue downstream, and high potential for both the helix and beta-fold) appear to be necessary but not sufficient, as some otherwise promising sequences found in data bank searches proved not to be capable of cooperative refolding. Analysis of existing switches has led to the development of the side chain interaction index (SCII) as a further parameter characterizing the beta --> alpha polarity-driven switch. Data bank searches using this additional parameter have successfully identified a series of new potential switch sequences. All of them have in common the amino acid tetrad LPCR at the N-terminus and a tryptophan 5-20 residues C-terminal to it. Those with a high SCII as well, when synthesized and tested, exhibited strongly cooperative polarity-driven refolding. Control peptides, containing all other parameters but with a low SCII, did not. Using this new information, an artificial sequence was designed that had a high SCII as well as the initiation site, conserved tryptophan, and high Palpha and Pbeta. When synthesized and tested, this sequence did in fact behave as a conformational switch, refolding cooperatively from beta-fold to helix at a threshold value of 30% TFE. The successful design of a polarity-driven conformational switch opens the possibility of using this motif as a tool in protein engineering.

Adenylyl Cyclases↗
PubMed1997

Immunosuppressor binding to the immunophilin FKBP59 affects the local structural dynamics of a surface beta-strand: time-resolved fluorescence study.

The interaction of the immunophilin domain of FKBP59 (FKBP59-I) with immunosuppressant drugs was investigated by steady-state and time-resolved fluorescence of tryptophan. One of the two Trp residues present in this protein (W89), conserved in almost all immunophilins, is buried in the hydrophobic core and participates in the immunosuppressant binding. By comparison with the highly homologous protein FKBP12, containing only the buried Trp, it has been concluded that its weak fluorescence is due to an atypical H-bond interaction involving the indole nitrogen and the Phe129 benzene ring. The second Trp residue (W59) in FKBP59-I is located on the external hydrophilic side of the 50-60 beta-sheet [Craescu, C. T., Rouvière, N., Popescu, A., Cerpolini, E., Lebeau, M.-C., Baulieu, E.-E., & Mispelter, J. (1996) Biochemistry 35, 11045-11052] and is responsible for >95% of the fluorescence emission. The long lifetime of the major excited state, the large activation energy of thermal quenching, and the rotational correlation time distribution pattern suggest that its environment is not highly mobile. Binding of the immunosuppressant drugs FK506 and rapamycin leads to a approximately 60% decrease of the fluorescence intensity without any change in the fluorescence emission maximum. Time-resolved measurements show that this "quenching" is due to a conformational change which depletes the long excited-state lifetime population to the profit of a more quenched minor excited state, which becomes prominent in the complexes. This is accompanied by a strong slowing of the indole ring dynamics in the case of FK506 and by a complete immobilization in the case of rapamycin, as shown by two-dimensional (tau, theta) maximum entropy analysis of the polarized fluorescence decays. Binding of the immunosuppressant drugs therefore modifies the structure and the dynamics of the external side of the 50-60 beta-sheet in FKBP59-I, which could be relevant for the formation of ternary complexes with other protein targets.

Acrylamide↗
PubMed2000

Partial molecular alignment via local structure analysis

Molecular alignment remains as one of the most problematic aspects of molecular design. A technique is introduced that facilitates the alignment of a range of structures that could not be handled easily using existing alignment procedures. The flexibility of the method is illustrated with a series of test sets. First, an alignment is performed on a series of molecules from a typical 3D-quantitative structure-activity relationship data set. The results of this test show the technique to outperform many existing alignment methodologies based upon the optimization of molecular similarity of molecular overlaps. This test set is then extended to consider the alignment of more structurally diverse inhibitors of HIV-1 reverse transcriptase and HIV-1 protease. Finally, in the most challenging test, a large protein-based inhibitor is matched with a small-molecule mimic. It is believed that the existence of such a versatile alignment technique will prove invaluable in the fields of molecular design and chemical information handling.

Journal Article↗
PubMed2001

Local structure and tunneling kinetics of ammonium aluminum alum by infrared hole-burning.

The title compound, crystallized with a few percent of deuterium, contains some NH(3)D(+) and HOD. At low temperatures, five N-D stretch bands are observed. These belong to two ammonium sites with apparent C(s) symmetry in the low-temperature phase. The N-D bands can be hole-burned with an infrared laser. Burning bands belonging to the A-sites transforms some of them to the higher-energy B-sites. The A- and B-sites probably differ from each other by the arrangement of water and sulfate about the ammonium.

Journal Article↗
PubMed2004

Local structure and charge distribution in the UO(2)-U(4)O(9) system.

Analysis of X-ray absorption fine structure spectra of UO(2+x) for x = 0-0.20 (UO(2)--U(4)O(9)) reveals that the adventitious O atoms are incorporated as oxo groups with U--O distances of 1.74 A, most likely associated with U(VI), that occur in clusters so that the UO(2) fraction of the material largely remains intact. In addition to the formation of some additional longer U--O bonds, the U sublattice consists of an ordered portion that displays the original U--U distance and a spectroscopically silent, glassy part. This is very different from previous models derived from neutron diffraction that maintained long U--O distances and high U--O coordination numbers. UO(2+x) also differs from PuO(2+x) in its substantially shorter An-oxo distances and no sign of stable coordination with H(2)O and its hydrolysis products.

Journal Article↗
PubMed2005

Local structure and near-infrared emission features of neodymium-based amine functionalized organic/inorganic hybrids.

Nd(3+)-based organic/inorganic hybrids have potential application in the field of integrated optics. Attractive sol-gel derived di-urea and di-urethane cross-linked poly(oxyethylene) (POE)/siloxane hybrids (di-ureasils and di-urethanesils, respectively) doped with neodymium triflate (Nd(CF(3)SO(3))(3)) were examined by Fourier transform mid-infrared (FT-IR), Raman (FT-Raman), (29)Si magic-angle spinning (MAS) nuclear magnetic resonance (NMR) and photoluminescence spectroscopies, and small-angle X-ray scattering (SAXS). The goals of this work were to determine which cation coordinating site of the host matrix (ether oxygen atoms or carbonyl oxygen atoms) is active in each of the materials analyzed, its influence on the nanostructure of the samples and its relation with the photoluminescence properties. The main conclusion derived from this study is that the hydrogen-bonded associations formed throughout the materials play a major role in the hybrids nanostructure and photoluminescence properties.

Journal Article↗
PubMed2005

Probing the local structure and mechanical response of nanostructures using force modulation and nanofabrication.

Nanostructures of self-assembled monolayers (SAMs) are designed and produced using coadsorption and nanografting techniques. Because the structures of these artificially engineered domains are predesigned and well-characterized, a systematic investigation is possible to study the mechanical responses to force modulation under atomic force microscope tips. Force modulation imaging reveals characteristic contrast sensitivity to changes in molecular-level packing, molecule chain lengths, domain boundaries, and surface chemical functionalities in SAMs. By means of actively tuning the driving frequency, the resonances at the tip-surface contact are selectively activated. Therefore, specific surface features, such as the edges of the domains and nanostructures or desired chemical functionalities, can be selectively enhanced in the amplitude images. These observations provide a new and active approach in materials characterization and the study of nanotribology using atomic force microscopy.

Journal Article↗
PubMed2006

Quantitative adsorption and local structures of gallium(III) at the water-alpha-FeOOH interface.

The adsorption of Ga(III) at the water-alpha-FeOOH (goethite) interface has been investigated by means of quantitative adsorption experiments, extended X-ray absorption fine structure (EXAFS) spectroscopy, and surface complexation modeling. Under the conditions studied, pH range 3-11 and surface coverages of 0.9-3.2 micromol/m2, Ga(III) was found to adsorb strongly to alpha-FeOOH, and the surface species were more resistant toward hydrolysis and formation of soluble Ga(OH)4- than either solid gallium hydroxides or soluble polynuclear complexes. The EXAFS measurements revealed the presence of octahedral Ga(III) complexes at the water-alpha-FeOOH interface, with practically no structural variations as a function of pH or total gallium concentration. Analysis of the first coordination shell required an anharmonic model indicating a distorted geometry of the GaO6 octahedra, with mean Ga-O distances at 1.96-1.98 angstroms. A method based on the continuous Cauchy wavelet transforms (CCWT) was used to identify backscattering atoms in the higher coordination shells. This analysis indicated predominately Fe backscattering, and the quantitative data fitting resulted in three Ga-Fe paths at 3.05, 3.2, and 3.55 angstroms, which correspond to two edge-sharing and one corner-sharing linkage, respectively. The collective results from EXAFS spectroscopy showed that Ga(III) adsorbs to Fe equivalent sites at the surface alpha-FeOOH as an extension of the rows of Fe octahedra in the bulk structure. This interpretation was further corroborated by a Ga-Fe-Fe multiple scattering path at 6.13 angstroms. The quantitative adsorption and proton data were modeled using a surface complexation formalism based on a 1 pK(a) constant capacitance model. In agreement with the EXAFS results, the model obtained included one predominating surface complex with the stoichiometry [triple bond]FeOGa(OH)2(-0.5) and the stability constant log beta(intr.) = -2.55 +/- 0.04 ([triple bond]FeOH(-0.5) + Ga3+ + 2H2O <--> [triple bond]FeOGa(OH)2(-0.5) + 3H+).

Adsorption↗
PubMed2004

Local structural balance and functional interaction of excitatory and inhibitory synapses in hippocampal dendrites.

Theoretical and experimental studies on the computation of neural networks suggest that neural computation results from a dynamic interplay of excitatory and inhibitory (E/I) synaptic inputs. Precisely how E/I synapses are organized structurally and functionally to facilitate meaningful interaction remains elusive. Here we show that E/I synapses are regulated across dendritic trees to maintain a constant ratio of inputs in cultured rat hippocampal neurons. This structural arrangement is accompanied by an E/I functional balance maintained by a 'push-pull' feedback regulatory mechanism that is capable of adjusting E/I efficacies in a coordinated fashion. We also found that during activity, inhibitory synapses can determine the impact of adjacent excitatory synapses only if they are colocalized on the same dendritic branch and are activated simultaneously. These fundamental relationships among E/I synapses provide organizational principles relevant to deciphering the structural and functional basis for neural computation within dendritic branches.

Animals↗
PubMed1992

Inositol monophosphatase is a highly conserved enzyme having localized structural similarity to both glycerol 3-phosphate dehydrogenase and haemoglobin.

The cDNA coding for an inositol monophosphatase in the oocytes of the African clawed frog, Xenopus laevis, has been isolated and sequenced. The predicted primary structure of this enzyme is markedly conserved when it is compared with its mammalian functional homologues; up to 84% of the amino acid residues are identical, and conservative substitutions increase the similarity to 95%, suggesting that this sequence represents the most parsimonious primary structure for the protein to maintain not only catalytic activity but also perhaps the facility to interact with other macromolecules. Two regions of the protein, each of about 11 residues and separated by about 90 residues, have been identified as a consensus found also in glycerol 3-phosphate dehydrogenase (EC 1.1.1.8). One of these regions is also found to be particularly conserved in the alpha-globin of birds and reptiles; birds and some turtles are known to modulate the oxygen affinity of their haemoglobin with inositol polyphosphate in the same way as with 2,3-bisphosphoglycerate in other species. This region is also conserved in the beta-globin of most species, beginning with lysine-82, which is known to participate in the binding of organic phosphates. These regions of the inositol monophosphatase may represent motifs for the binding of its substrate.

Amino Acid Sequence↗