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PubMed2006

Jet cooled spectroscopy of H2DO+: Barrier heights and isotope-dependent tunneling dynamics from H3O+ to D3O+.

The first high resolution spectroscopic data for jet cooled H2DO+ are reported, specifically via infrared laser direct absorption in the OH stretching region with a slit supersonic jet discharge source. Transitions sampling upper (0-) and lower (0+) tunneling states for both symmetric (nu1+ <-- 0+, nu1- <-- 0-, and nu1- <-- 0+) and antisymmetric (nu3+ <-- 0+ and nu3- <-- 0-) OH stretching bands are observed, where +/- refers to wave function reflection symmetry with respect to the planar umbrella mode transition state. The spectra can be well fitted to a Watson asymmetric top Hamiltonian, revealing band origins and rotational constants for benchmark comparison with high-level ab initio theory. Of particular importance are detection and assignment of the relatively weak band (nu1- <-- 0+) that crosses the inversion tunneling gap, which is optically forbidden in H3O+ or D3O+, but weakly allowed in H2DO+ by lowering of the tunneling transition state symmetry from D(3h) to C(2v). In conjunction with other H2DO+ bands, this permits determination of the tunneling splittings to within spectroscopic precision for each of the ground [40.518(10) cm(-1)], nu1 = 1 [32.666(6) cm(-1)], and nu3 = 1 [25.399(11) cm(-1)] states. A one-dimensional zero-point energy corrected potential along the tunneling coordinate is constructed from high-level ab initio CCSD(T) calculations (AVnZ, n = 3,4,5) and extrapolated to the complete basis set limit to extract tunneling splittings via a vibrationally adiabatic treatment. Perturbative scaling of the potential to match splittings for all four isotopomers permits an experimental estimate of DeltaV0 = 652.9(6) cm(-1) for the tunneling barrier, in good agreement with full six-dimensional ab initio results of Rajamaki, Miani, and Halonen (RMH) [J. Chem. Phys. 118, 10929 (2003)]. (DeltaV0 (RMH) = 650 cm(-1)). The 30%-50% decrease in tunneling splitting observed upon nu1 and nu3 vibrational excitations arises from an increase in OH stretch frequencies at the planar transition state, highlighting the transition between sp2 and sp3 hybridizations of the OHD bonds as a function of inversion bending angle.

Journal Article↗
PubMed2001

Management of facial paralysis resulting from temporal bone fractures: Our experience in 115 cases.

OBJECTIVE: The goal of this study was to review decision factors and overall results regarding surgical and nonsurgical management of post-traumatic facial nerve paralysis (FP). STUDY DESIGN: A retrospective study and literature review were performed. METHODS: Between 1984 and 1990, 115 cases of post-traumatic FP were handled. Patients were evaluated through clinical, audiologic, radiologic, and electromyogram assessment. Depending on examination results, patients were treated either medically or surgically through total facial nerve decompression. RESULTS: Forty-nine of the 50 medically treated patients experienced a normal or subnormal facial function recovery (grade I-II). Of the 65 (56.5%) surgically treated patients, 52 (80%) had immediate, 2 had delayed, and 11 (17%) had unknown delay-associated FP. The approaches chosen were middle fossa and transmastoid (75.3%), translabyrinthine (10.7%), or pure transmastoid according to facial nerve nonmotor branch evaluation, hearing, location of the fracture line, and the patient's general condition. Lesions were predominantly found in the geniculate ganglion area (66.2%). A nerve gap was found in only 13.8% of the cases. At 2 years after surgery, 93.8% had a grade I to III recovery. None had grade V or VI. CONCLUSION: The rarity of severe nerve lesions encountered in surgically treated patients raises the question of better selection of candidates for surgery. Surgery is clearly indicated when FP is total, is of immediate onset, and is associated with a bad prognosis electromyogram pattern. In other settings, decisions are to be made based on high-resolution CT data and electromyogram results, thanks to a clinical survey and second electromyogram evaluation.

Adolescent↗
PubMed2001

Investigation of skeletal muscle denervation and reinnervation using magnetic resonance spectroscopy.

OBJECTIVE: To determine changes in skeletal muscle metabolism after nerve transection and repair and to correlate metabolic changes with functional recovery. STUDY DESIGN AND SETTING: Male Wistar rats were divided into 6 experimental groups plus a control group. The posterior tibial nerve was transected and reapproximated. At varying times after surgery (1, 2, 4, 6, or 8 weeks) animals were sacrificed, the gastrocnemius muscle was harvested, and proton nuclear magnetic resonance (NMR) spectroscopy was performed. Functional recovery was measured using the sciatic function index. RESULTS: Animals undergoing nerve repair all showed functional recovery whereas the nonrepaired nerve group did not. Concentration of glucose and lactate increased after denervation and then returned toward normal. Choline concentration decreased and then returned toward normal. In animals not undergoing nerve repair, the metabolic abnormalities persisted and showed no sign of recovery over the 8-week observation period. CONCLUSIONS: 1H NMR spectroscopy is a potentially useful tool to study changes in skeletal muscle metabolism after motor nerve injury. SIGNIFICANCE: NMR spectroscopy is rapidly developing into a clinically useful tool. High-field magnets have improved resolution and data acquisition. Basic experiments, such as those described here, will help guide the use of NMR spectroscopy in clinical medicine and will also lead to a better understanding of basic mechanisms of nerve injury and repair.

Action Potentials↗
PubMed2004

High-resolution vegetation and climate change associated with Pliocene Australopithecus afarensis.

Plio-Pleistocene global climate change is believed to have had an important influence on local habitats and early human evolution in Africa. Responses of hominin lineages to climate change have been difficult to test, however, because this procedure requires well documented evidence for connections between global climate and hominin environment. Through high-resolution pollen data from Hadar, Ethiopia, we show that the hominin Australopithecus afarensis accommodated to substantial environmental variability between 3.4 and 2.9 million years ago. A large biome shift, up to 5 degrees C cooling, and a 200- to 300-mm/yr rainfall increase occurred just before 3.3 million years ago, which is consistent with a global marine delta(18)O isotopic shift.

Animals↗
PubMed2005

De novo design of an IL-4 antagonist and its structure at 1.9 A.

An IL-4 antagonist was designed based on structural and biochemical analysis of unbound IL-4 and IL-4 in complex with its high-affinity receptor (IL-4Ralpha). Our design strategy sought to capture a protein-protein interaction targeting the high affinity that IL-4 has for IL-4Ralpha. This strategy has impact due to the potential relevance of IL-4Ralpha as a drug target in the treatment of asthma. To mimic the IL-4 binding surface, critical side chains for receptor binding were identified, and these side chains were transplanted onto a previously characterized, de novo-designed four-helix protein called designed helical protein 1 (DHP-1). This first-generation design resolved the ambiguity previously described for the connectivity between helices in DHP-1 and resulted in a protein capable of binding to IL-4Ralpha. The second-generation antagonist was based upon further molecular modeling, and it succeeded in binding IL-4Ralpha better than the first-generation. This protein, termed DHP-14-AB, yielded a protein with a cooperative unfolding transition (DeltaGu0=8.1 kcal/mol) and an IC50 of 27 microM when in competition with IL-4 whereas DHP-1 had no affinity for IL-4Ralpha. The crystal structure of DHP-14-AB was determined to 1.9-A resolution and was compared with IL-4. This comparison revealed how design strategies targeting protein-protein interactions require high-resolution 3D data and the incorporation of orientation-specific information at the level of side-chains and secondary structure element interactions.

Binding Sites↗
PubMed2005

Soluble epoxide hydrolase is a therapeutic target for acute inflammation.

As of 2004, >73 million people were prescribed antiinflammatory medication. Despite the extensive number of current products, many people still suffer from their diseases or the pharmacological properties (side effects) of the medications. Therefore, developing therapeutic strategies to treat inflammation remains an important endeavor. Here, we demonstrate that the soluble epoxide hydrolase (sEH) is a key pharmacologic target for treating acute systemic inflammation. Lipopolysaccharide-induced mortality, systemic hypotension, and histologically evaluated tissue injury were substantially diminished by administration of urea-based, small-molecule inhibitors of sEH to C57BL/6 mice. Moreover, sEH inhibitors decreased plasma levels of proinflammatory cytokines and nitric oxide metabolites while promoting the formation of lipoxins, thus supporting inflammatory resolution. These data suggest that sEH inhibitors have therapeutic efficacy in the treatment and management of acute inflammatory diseases.

Adamantane↗
PubMed2003

Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex.

The utilization of organized supramolecular assemblies to exploit the synergistic interactions afforded by close proximity, both for enzymatic synthesis and for the degradation of recalcitrant substrates, is an emerging theme in cellular biology. Anaerobic bacteria harness a multiprotein complex, termed the "cellulosome," for efficient degradation of the plant cell wall. This megadalton catalytic machine organizes an enzymatic consortium on a multifaceted molecular scaffold whose "cohesin" domains interact with corresponding "dockerin" domains of the enzymes. Here we report the structure of the cohesin-dockerin complex from Clostridium thermocellum at 2.2-A resolution. The data show that the beta-sheet cohesin domain interacts predominantly with one of the helices of the dockerin. Whereas the structure of the cohesin remains essentially unchanged, the loop-helix-helix-loop-helix motif of the dockerin undergoes conformational change and ordering compared with its solution structure, although the classical 12-residue EF-hand coordination to two calcium ions is maintained. Significantly, internal sequence duplication within the dockerin is manifested in near-perfect internal twofold symmetry, suggesting that both "halves" of the dockerin may interact with cohesins in a similar manner, thus providing a higher level of structure to the cellulosome and possibly explaining the presence of "polycellulosomes." The structure provides an explanation for the lack of cross-species recognition between cohesin-dockerin pairs and thus provides a blueprint for the rational design, construction, and exploitation of these catalytic assemblies.

Amino Acid Sequence↗
PubMed1991

Water structure in cubic insulin crystals.

The electron density distribution of the solvent in the cubic insulin crystal structure, which occupies 65% of the volume, has been mapped from 1.7-A resolution diffraction data by an iterative difference Fourier method, using the previously determined protein structure as the refinement restraint. Starting with phases from the protein and a flat solvent model, the difference map calculated from the data was added outside the protein envelope, and the modified map was then used to recalculate phases for the iterative refinement. Tests of the method with model data, with the experimental data and a variant protein model, and by carrying out a partial refinement of the solvent map demonstrate that the refinement algorithm produces reliable values for the solvent density within the noise level of the data. Fluctuations in density are observed throughout the solvent space, demonstrating that nonrandom arrangements of the water molecules extend several layers from the well-ordered hydration shell in contact with the protein surface. Such ordering may account for the hydration force opposing close approach of hydrophilic surfaces and other long-range water-dependent interactions in living structures.

Fourier Analysis↗
PubMed1995

Determination of helix-helix interactions in membranes by rotational resonance NMR.

Dimerization of human glycophorin A in erythrocyte membranes is mediated by specific interactions within the helical transmembrane domain of the protein. Rotational resonance NMR provides a unique approach for obtaining high-resolution structural data in membrane systems and has been used to establish intermolecular contacts in the glycophorin A dimer by using hydrophobic peptides that correspond to the transmembrane sequence. Magnetization exchange rates were measured between [13C]methyl labels in the hydrophobic sequence -G79-V80-M81-A82-G83-V84- located in the middle of the transmembrane domain and specific [13C]carbonyl labels along the peptide backbone across the dimer interface. Significant magnetization exchange was observed only between V80 (13CH3) and G79 (13C = O) and between V84 (13CH3) and G83 (13C = O), indicating that these residues are packed in the dimer interface in a "ridges-ingrooves" arrangement.

Amino Acid Sequence↗
PubMed1995

X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia B.

Hereditary deficiency of factor IXa (fIXa), a key enzyme in blood coagulation, causes hemophilia B, a severe X chromosome-linked bleeding disorder afflicting 1 in 30,000 males; clinical studies have identified nearly 500 deleterious variants. The x-ray structure of porcine fIXa described here shows the atomic origins of the disease, while the spatial distribution of mutation sites suggests a structural model for factor X activation by phospholipid-bound fIXa and cofactor VIIIa. The 3.0-A-resolution diffraction data clearly show the structures of the serine proteinase module and the two preceding epidermal growth factor (EGF)-like modules; the N-terminal Gla module is partially disordered. The catalytic module, with covalent inhibitor D-Phe-1I-Pro-2I-Arg-3I chloromethyl ketone, most closely resembles fXa but differs significantly at several positions. Particularly noteworthy is the strained conformation of Glu-388, a residue strictly conserved in known fIXa sequences but conserved as Gly among other trypsin-like serine proteinases. Flexibility apparent in electron density together with modeling studies suggests that this may cause incomplete active site formation, even after zymogen, and hence the low catalytic activity of fIXa. The principal axes of the oblong EGF-like domains define an angle of 110 degrees, stabilized by a strictly conserved and fIX-specific interdomain salt bridge. The disorder of the Gla module, whose hydrophobic helix is apparent in electron density, can be attributed to the absence of calcium in the crystals; we have modeled the Gla module in its calcium form by using prothrombin fragment 1. The arched module arrangement agrees with fluorescence energy transfer experiments. Most hemophilic mutation sites of surface fIX residues occur on the concave surface of the bent molecule and suggest a plausible model for the membrane-bound ternary fIXa-FVIIIa-fX complex structure: fIXa and an equivalently arranged fX arch across an underlying fVIIIa subdomain from opposite sides; the stabilizing fVIIIa interactions force the catalytic modules together, completing fIXa active site formation and catalytic enhancement.

Amino Acid Chloromethyl Ketones↗
PubMed1996

Receptor up-regulation, internalization, and interconverting receptor states. Critical components of a quantitative description of N-formyl peptide-receptor dynamics in the neutrophil.

High resolution kinetic data of the binding of fluorescent peptide to the N-formyl peptide receptor of neutrophils at 37 degrees C has allowed for the development of a ligand binding model that predicts statistically larger binding rate constants than those previously reported for intact neutrophils. The new model accounts for ligand association and dissociation, receptor up-regulation, ligand-receptor complex internalization, a change in receptor affinity, and the quenching of internalized fluorescent ligand. We determined that receptor up-regulation is both agonist- and temperature-induced and is inhibited by both phenylarsine oxide and pertussis toxin treatment. Model fits of ligand association to pertussis toxin-treated cells show that while receptor up-regulation was inhibited, rate constants for ligand binding, receptor affinity conversion, and internalization of ligand-receptor complexes were unaffected. Results suggest Gi-protein-mediated receptor up-regulation and Gi-protein-independent receptor affinity conversion. Simulation of ligand infusion using our model gives insight into the quantitative and dynamic relationship between the low affinity ligand-receptor complex and the actin polymerization response.

Amino Acid Sequence↗
PubMed1997

Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications.

The structures of oxidized, reduced, nitrite-soaked oxidized and nitrite-soaked reduced nitrite reductase from Alcaligenes faecalis have been determined at 1.8-2.0 A resolution using data collected at -160 degrees C. The active site at cryogenic temperature, as at room temperature, contains a tetrahedral type II copper site liganded by three histidines and a water molecule. The solvent site is empty when crystals are reduced with ascorbate. A fully occupied oxygen-coordinate nitrite occupies the solvent site in crystals soaked in nitrite. Ascorbate-reduced crystals soaked in a glycerol-methanol solution and nitrite at -40 degrees C remain colorless at -160 degrees C but turn amber-brown when warmed, suggesting that NO is released. Nitrite is found at one-half occupancy. Five new solvent sites in the oxidized nitrite bound form exhibit defined but different occupancies in the other three forms. These results support a previously proposed mechanism by which nitrite is bound primarily by a single oxygen atom that is protonable, and after reduction and cleavage of that N-O bond, NO is released leaving the oxygen atom bound to the Cu site as hydroxide or water.

Alcaligenes↗
PubMed2000

Multiple conformations of catalytic serine and histidine in acetylxylan esterase at 0.90 A.

Acetylxylan esterase (AXEII; 207 amino acids) from Penicillium purpurogenum has substrate specificities toward acetate esters of d-xylopyranose residues in xylan and belongs to a new class of alpha/beta hydrolases. The crystal structure of AXEII has been determined by single isomorphous replacement and anomalous scattering, and refined at 0.90- and 1.10-A resolutions with data collected at 85 K and 295 K, respectively. The tertiary structure consists of a doubly wound alpha/beta sandwich, having a central six-stranded parallel beta-sheet flanked by two parallel alpha-helices on each side. The catalytic residues Ser(90), His(187), and Asp(175) are located at the C-terminal end of the sheet, an exposed region of the molecule. The serine and histidine side chains in the 295 K structure show the frequently observed conformations in which Ser(90) is trans and the hydroxyl group is in the plane of the imidazole ring of His(187). However, the structure at 85 K displays an additional conformation in which Ser(90) side-chain hydroxyl is away from the plane of the imidazole ring of His(187). The His(187) side chain forms a hydrogen bond with a sulfate ion and adopts an altered conformation. The only other known hydrolase that has a similar tertiary structure is Fusarium solani cutinase. The exposed nature of the catalytic triad suggests that AXEII is a pure esterase, i.e. an alpha/beta hydrolase with specificity for nonlipidic polar substrates.

Acetylesterase↗
PubMed2001

Structure of human thymidylate synthase suggests advantages of chemotherapy with noncompetitive inhibitors.

Thymidylate synthase (TS) is a major target in the chemotherapy of colorectal cancer and some other neoplasms. The emergence of resistance to the treatment is often related to the increased levels of TS in cancer cells, which have been linked to the elimination of TS binding to its own mRNA upon drug binding, a feedback regulatory mechanism, and/or to the increased stability to intracellular degradation of TS.drug complexes (versus unliganded TS). The active site loop of human TS (hTS) has a unique conformation resulted from a rotation by 180 degrees relative to its orientation in bacterial TSs. In this conformation, the enzyme must be inactive, because the catalytic cysteine is no longer positioned in the ligand-binding pocket. The ordered solvent structure obtained from high resolution crystallographic data (2.0 A) suggests that the inactive loop conformation promotes mRNA binding and intracellular degradation of the enzyme. This hypothesis is supported by fluorescence studies, which indicate that in solution both active and inactive forms of hTS are present. The binding of phosphate ion shifts the equilibrium toward the inactive conformation; subsequent dUMP binding reverses the equilibrium toward the active form. Thus, TS inhibition via stabilization of the inactive conformation should lead to less resistance than is observed with presently used drugs, which are analogs of its substrates, dUMP and CH(2)H(4)folate, and bind in the active site, promoting the active conformation. The presence of an extension at the N terminus of native hTS has no significant effect on kinetic properties or crystal structure.

Amino Acid Sequence↗
PubMed2003

Structural characterization of HC-Pro, a plant virus multifunctional protein.

The helper component proteinase (HC-Pro) is a key protein encoded by plant viruses of the genus Potyvirus. HC-Pro is involved in different steps of the viral cycle, aphid transmission, replication, and virus cell-to-cell and systemic movement and is a suppressor of post-transcriptional gene silencing. Structural knowledge of HC-Pro is required to better understand its multiple functions. To this aim, we purified His-tagged wild-type HC-Pro and a N-terminal deletion mutant (DeltaHC-Pro) from plants infected with recombinant potyviruses. Biochemical analysis of the recombinant proteins confirmed that HC-Pro is a dimer in solution, that the N terminus is not essential for self-interaction, and that a large C-terminal domain is highly resistant to proteolysis. Two-dimensional crystals of the recombinant proteins were successfully grown on Ni2+-chelating lipid monolayers. Comparison of projection maps of negatively stained crystals revealed that HC-Pro is composed of two domains separated by a flexible constriction. Cryo-electron crystallography of DeltaHC-Pro allowed us to calculate a projection map at 9-A resolution. Our data from electron microscopy, biochemical analysis, and secondary structure predictions lead us to suggest a model for structure/function relationships in the HC-Pro protein.

Cryoelectron Microscopy↗
PubMed2004

Structure and dynamics of a helical hairpin that mediates calcium-dependent membrane binding of annexin B12.

A wealth of high-resolution structural data has accumulated for soluble annexins, but only limited information is available for the biologically important membrane-bound proteins. To investigate the structural and dynamic changes that occur upon membrane binding, we analyzed the electron paramagnetic resonance (EPR) mobility and accessibility parameters of a continuous 30-residue nitroxide scan encompassing helices D and E in repeat 2 of annexin B12 (residues 134-163) while the protein was bound to phospholipid vesicles in the presence of Ca(2+). A comparison of these data to those from a previously published study of the protein in solution (Isas, J. M., Langen, R., Haigler, H. T., and Hubbell, W. L. (2002) Biochemistry 41, 1464-1473) showed that the overall backbone fold for the scanned region did not change upon membrane binding. However, side-chains in the loop between the D and E helices were highly dynamic in solution but became essentially frozen in the EPR time scale upon binding to membranes. Accessibility measurements clearly established that side-chains in this loop were exposed to the hydrophobic core of the bilayer and provide the first evidence that a D-E loop directly participates in the Ca(2+)-dependent binding of annexins to membranes. Other localized changes showed that the D-helix became much less dynamic after membrane binding and identified quaternary contact sites in the membrane-bound homo-trimer. Finally, immobilization of the D-E loop upon contact with phospholipid suggests that the bilayer, which is normally very mobile on the EPR time scale, is immobilized in the head-group region by the annexin B12. This suggests that annexin B12 alters membrane structure in a manner that may be biologically significant.

Annexins↗
PubMed2004

The structural basis of the thermostability of SP1, a novel plant (Populus tremula) boiling stable protein.

We previously reported on a new boiling stable protein isolated from aspen plants (Populus tremula), which we named SP1. SP1 is a stress-related protein with no significant sequence homology to other stress-related proteins. It is a 108-amino-acid hydrophilic polypeptide with a molecular mass of 12.4 kDa (Wang, W. X., Pelah, D., Alergand, T., Shoseyov, O., and Altman, A. (2002) Plant Physiol. 130, 865-875) and is found in an oligomeric form. Preliminary electron microscopy studies and matrix-assisted laser desorption ionization time-of-flight mass spectrometry experiments showed that SP1 is a dodecamer composed of two stacking hexamers. We performed a SDS-PAGE analysis, a differential scanning calorimetric study, and crystal structure determination to further characterize SP1. SDS-PAGE indicated a spontaneous assembly of SP1 to one stable oligomeric form, a dodecamer. Differential scanning calorimetric showed that SP1 has high thermostability i.e. Tm of 107 degrees C (at pH 7.8). The crystal structure of SP1 was initially determined to 2.4 A resolution by multi-wavelength anomalous dispersion method from a crystal belonging to the space group I422. The phases were extended to 1.8 A resolution using data from a different crystal form (P21). The final refined molecule includes 106 of the 108 residues and 132 water molecules (on average for each chain). The R-free is 20.1%. The crystal structure indicated that the SP1 molecule has a ferredoxin-like fold. Strong interactions between each two molecules create a stable dimer. Six dimers associate to form a ring-like-shaped dodecamer strongly resembling the particle visualized in the electron microscopy studies. No structural similarity was found between the crystal structure of SP1 and the crystal structure of other stress-related proteins such as small heat shock proteins, whose structure has been already determined. This structural study further supports our previous report that SP1 may represent a new family of stress-related proteins with high thermostability and oligomerization.

Amino Acid Sequence↗
PubMed2004

Charged amino acids of the N-terminal domain are involved in coupling binding and gating in alpha7 nicotinic receptors.

Binding of agonists to nicotinic acetylcholine receptors generates a sequence of conformational changes resulting in channel opening. Previously, we have shown that the aspartate residue Asp-266 at the M2-M3 linker of the alpha7 nicotinic receptor is involved in connecting binding and gating. High resolution structural data suggest that this region could interact with the so-called loops 2 and 7 of the extracellular N-terminal region. In this case, certain charged amino acids present in these loops could integrate together with Asp-266 and other amino acids, a mechanism involved in channel activation. To test this hypothesis, all charged residues in these loops, Asp-42, Asp-44, Glu-45, Lys-46, Asp-128, Arg-130, and Asp-135, were substituted with other amino acids, and expression levels and electrophysiological responses of mutant receptors were determined. Mutants at positions Glu-45, Lys-46, and Asp-135 exhibited poor or null functional responses to different nicotinic agonists regardless of significant membrane expression, whereas D128A showed a gain of function effect. Because the double reverse charge mutant K46D/D266K did not restore receptor function, a gating mechanism controlled by the pairwise electrostatic interaction between these residues is not likely. Rather, a network of interactions formed by residues Lys-46, Asp-128, Asp-135, Asp-266, and possibly others appears to link agonist binding to channel gating.

Amino Acid Substitution↗