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Structure and function of Cerebratulus lacteus neurotoxin B-IV: tryptophan-30 is critical for function while lysines-18, -19, -29, and -33 are not required.

The Cerebratulus lacteus B-toxins are a family of polypeptide neurotoxins known to bind to crustacean voltage-sensitive sodium channels. We have previously shown that in the most abundant homolog, toxin B-IV, Arg-17 in the N-terminal helix and a positive charge at position 25 in the loop region are essential for function. In this report, we target a tryptophan residue at position 30, as well as lysine residues found in both the N-terminal helix and loop regions by polymerase chain reaction mutagenesis, to determine their contributions to toxin activity. Substitution of Trp-30 with a serine causes a more than 40-fold reduction in specific toxicity, whereas replacement by tyrosine and phenylalanine is well tolerated. The secondary structures of both these muteins are identical to that of the wild-type toxin as determined by circular dichroism spectroscopy. Thermal denaturation experiments also show that their conformational stabilities are intact. These results demonstrate that an aromatic residue at this position is required for toxin function. Charge neutralizing substitutions of Lys-18 and Lys-19 located in the N-terminal helix have very little effect on toxicity, suggesting the nonessentiality of these residues. Similar results are also obtained for the charge neutralizing muteins for Lys-29 and Lys-33 in the loop region. Interestingly, reduction experiments demonstrate that both K29N and W30S are more sensitive to reducing agent than wild-type B-IV, raising the possibility that the loop sequence may modulate toxin stability.

Animals↗

Electronic transitions involved in the absorption spectrum and dual luminescence of tetranuclear cubane [Cu4I4(pyridine)4] cluster: a density functional theory/time-dependent density functional theory investigation.

We present a combined density functional theory (DFT)/time-dependent density functional theory (TDDFT) study of the geometry, electronic structure, and absorption and emission properties of the tetranuclear "cubane" Cu4I4py4 (py = pyridine) system. The geometry of the singlet ground state and of the two lowest triplet states of the title complex were optimized, followed by TDDFT excited-state calculations. This procedure allowed us to characterize the nature of the excited states involved in the absorption spectrum and those responsible for the dual emission bands observed for this complex. In agreement with earlier experimental proposals, we find that while in absorption the halide-to-pyridine charge-transfer excited state (XLCT*) has a lower energy than the cluster-centered excited state (CC*), a strong geometrical relaxation on the triplet cluster-centered state surface leads to a reverse order of the excited states in emission.

Journal Article↗

Oxygen economy of cytochrome P450: what is the origin of the mixed functionality as a dehydrogenase-oxidase enzyme compared with its normal function?

The economy of dioxygen consumption by enzymes constitutes a fundamental problem in enzymatic chemistry (ref 1). Sometimes, the enzyme converts ALL the oxygen into water, without affecting the organic substrate, thereby acting as an "oxidase" (ref 1). Other times, the enzyme converts all the oxygen into water and causes desaturation in the substrate, thus exhibiting a mixed function as both "oxidase" and "dehydrogenase" (refs 2-5). The present paper describes density functional calculations demonstrating that the oxidase-dehydrogenase mixed activity occurs from the cationic intermediate species and requires electro-steric inhibition of the rebound process. Furthermore, the calculations reveal that the carbocation is formally nascent from an excited state of the active species of the enzyme (2Cpd I), in which the Fe=O moiety is singlet coupled as in the 1Deltag state of dioxygen! Thus, our results resolve an important mechanism and reveal the factors that underlie its observability.

Catalysis↗

Covalent attachment of acetylene and methylacetylene functionality to Si(111) surfaces: scaffolds for organic surface functionalization while retaining Si-C passivation of Si(111) surface sites.

Si(111) surfaces have been functionalized with Si-CC-R species, where R = H or -CH3, using a two-step reaction sequence involving chlorination of H-Si(111) followed by treatment with Na-CC-H or CH3-CC-Na reagents. The resulting surfaces showed no detectable oxidation as evidenced by X-ray photoelectron spectroscopic (XPS) data in the Si 2p region, electrochemical measurements of Si-H oxidation, or infrared spectroscopy. The Si-CC-R-terminated surfaces exhibited a characteristic CC stretch in the infrared at 2179 cm-1, which was strongly polarized perpendicular to the Si(111) surface plane. XPS measurements in the C 1s region showed a low binding energy peak indicative of Si-C bonding, with a coverage that was, within experimental error, identical to that of the CH3-terminated Si(111) surface, which has been shown to fully terminate the Si atop sites on an unreconstructed Si(111) surface. The Si-CC-H-terminated surfaces were further functionalized by exposure to n-C4H9Li followed by exposure to para Br-C6H5-CF3, allowing for introduction of para -C6H5CF3 groups while maintaining the desirable chemical and electrical properties that accompany complete Si-C termination of the atop sites on the Si(111) surface.

Journal Article↗

Syntheses of hexakis(4-functionalized-phenyl)benzenes and hexakis[4-(4'-functionalized- phenylethynyl)phenyl]benzenes directed to host molecules for guest-inclusion networks.

The syntheses of various types of hexakis(4-functionalized-phenyl)benzenes 1 and hexakis[4-(4'-functionalized-phenylethynyl)phenyl]benzenes 2 by the cobalt-catalyzed cyclotrimerization of diarylacetylenes and by the Sonogashira coupling reaction of 1e with arylacetylenes, respectively, are described. X-ray crystallographic analysis showed that host 1e or 2f forms a 2-D network by unique I...I or CH...O=C interactions, respectively.

Journal Article↗

Absorption spectra of caffeic acid, caffeate and their 1:1 complex with Al(III): density functional theory and time-dependent density functional theory investigations.

The UV-visible absorption spectra of caffeic acid, caffeate and of the predominant complex obtained in the presence of aluminum ion (1:1 stoichiometry) have been simulated by using the time-dependent density functional theory (TD-DFT) technique, taking into account solvent effects. Whereas the use of the B3LYP hybrid XC functional with the 6-31+G(d,p) basis set allows us to reproduce fairly well the essential features of the experimental spectra of caffeic acid and caffeate, it is necessary to introduce an effective core potential to properly describe the aluminum ion and its environment and to obtain a good agreement between theoretical and experimental spectra of the 1:1 complex. The ligand presents two potential complexing sites in competition. The results of our calculations show that the aluminum ion coordinates preferentially at the level of the catecholate group, and the [Al(H(2)O)(4)(CA)], [Al(H(2)O)(3)(OH)(CA)](-) and [Al(H(2)O)(4)(HCA)](+) complexed forms could coexist in aqueous solution at pH = 5.

Journal Article↗

Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.

We report the modification and parametrization of the united-residue (UNRES) force field for energy-based protein structure prediction and protein folding simulations. We tested the approach on three training proteins separately: 1E0L (beta), 1GAB (alpha), and 1E0G (alpha + beta). Heretofore, the UNRES force field had been designed and parametrized to locate native-like structures of proteins as global minima of their effective potential energy surfaces, which largely neglected the conformational entropy because decoys composed of only lowest-energy conformations were used to optimize the force field. Recently, we developed a mesoscopic dynamics procedure for UNRES and applied it with success to simulate protein folding pathways. However, the force field turned out to be largely biased toward -helical structures in canonical simulations because the conformational entropy had been neglected in the parametrization. We applied the hierarchical optimization method, developed in our earlier work, to optimize the force field; in this method, the conformational space of a training protein is divided into levels, each corresponding to a certain degree of native-likeness. The levels are ordered according to increasing native-likeness; level 0 corresponds to structures with no native-like elements, and the highest level corresponds to the fully native-like structures. The aim of optimization is to achieve the order of the free energies of levels, decreasing as their native-likeness increases. The procedure is iterative, and decoys of the training protein(s) generated with the energy function parameters of the preceding iteration are used to optimize the force field in a current iteration. We applied the multiplexing replica-exchange molecular dynamics (MREMD) method, recently implemented in UNRES, to generate decoys; with this modification, conformational entropy is taken into account. Moreover, we optimized the free-energy gaps between levels at temperatures corresponding to a predominance of folded or unfolded structures, as well as to structures at the putative folding-transition temperature, changing the sign of the gaps at the transition temperature. This enabled us to obtain force fields characterized by a single peak in the heat capacity at the transition temperature. Furthermore, we introduced temperature dependence to the UNRES force field; this is consistent with the fact that it is a free-energy and not a potential energy function. beta

Biophysics↗

Nonradical mechanisms for the uncatalyzed thermal functionalization of silicon surfaces by alkenes and alkynes: a density functional study.

We propose a new concerted mechanism for the uncatalyzed hydrosilylation of terminal alkenes and alkynes, alternative to the conventional radical-based mechanism. Density functional calculations have been carried out on these and on previously proposed alternative mechanisms for the hydrosilylation of ethylene and acetylene by suitable finite size clusters as models of the thermal functionalization of -SiH3, =SiH2, and [triple bound] SiH groups in flat Si(100) and Si(111) and porous silicon surfaces by alkenes and alkynes. For each step involved in the considered hydrosilylation pathways, we optimized the geometries of reactants and products and located the corresponding transition states. The calculated activation energies for the concerted pathways of ethylene and acetylene are, respectively, 57.6 and 60.9 kcal mol(-1) on -SiH3 and in the ranges 62-63 and 58-61 kcal mol-1 on =SiH2 and 64-66 and 56-61 kcal mol(-1) on SiH. These values are much lower than the activation energies calculated for the corresponding homolytic dissociation of the Si-H bond, which is the preliminary step in the radical path, 85.6, 82-83, and 79-81 kcal mol(-1), respectively, for -SiH3, =SiH2, and [triple bound] SiH groups. Our results thus suggest that the thermal hydrosilylation of alkenes and alkynes on silicon surfaces, for which a radical-based mechanism is currently accepted, may occur through a concerted mechanism.

Acetylene↗

Functional capacity evaluations in persons with spinal disorders: predicting poor outcomes on the Functional Assessment Screening Test (FAST).

This study determines how performance on the simple, low exertion Functional Assessment Screening Test (FAST) relates to performance on more extensive physical and psychological testing. One hundred eighty-eight persons with chronic back disability and 17 spine healthy volunteers underwent the FAST (three 2-min static tests [kneeling, stooping, and squatting] and two 5-min tests [repetitive stooping and repetitive twisting while standing]), the Progressive Isoinertial Lifting Evaluation (PILE), trunk extension endurance, submaximal bicycle ergometry, and psychological profiles. All FAST components were completed by 88% of spine healthy subjects, but only by 19.7% (n = 37) of the back patients. Internal consistency for overall test performance was 0.82 (alpha coefficient). Back pain noncompleters had poorer performance on the PILE and trunk extension endurance despite similar cardiovascular fitness and perceived exertion during testing. They had more dysfunctional coping mechanisms, pain avoidance, depression, and self-reported disability. Since performance on nonstrenuous testing is so poor, and psychosocial variables relate strongly to test performance, extensive Functional Capacity Evaluations may not be necessary or valid in assessing the physical performance of this population of chronic back pain patients.

Activities of Daily Living↗

Coagulation protein function VII: diametric effects of acetaldehyde on factor VII and factor IX function.

The first metabolite of ethanol, acetaldehyde, has the ability to form adducts with proteins and alter their function. It has been shown that acetaldehyde reacts with various proteins of the blood coagulation pathway and, subsequently, produces a prolongation of the clotting time. This study evaluated the function of clotting proteins from the extrinsic coagulation pathway (factor VII) and the intrinsic coagulation pathway (factor IX) when preincubated with acetaldehyde as compared to a control and compared to preincubation with ethanol. Prior to use in a clotting assay, incubation times with acetaldehyde, ethanol, and the control were the same for both factors VII and IX. An automatic fibrometer measured the clotting times. Factor VII preincubated with acetaldehyde prolonged the clotting time. However, factor IX preincubated with acetaldehyde actually decreased the clotting time. Of interest, both factors VII and IX preincubated with acetaldehyde produced statistically significant results when compared to the control and ethanol. This experiment indicates that acetaldehyde, in forming an adduct with proteins of the blood coagulation pathway, may induce a conformational change of factors VII and IX so as to either increase or decrease the clotting time. Therefore, it is possible that some of the deranged coagulation in alcohol abusers may be a final net result of the interaction of acetaldehyde and proteins of the coagulation pathway.

Acetaldehyde↗

Assessment of bone marrow stem cell reserve and function and stromal cell function in patients with severe congenital neutropenia.

OBJECTIVE: To investigate further the cellular defect responsible for impaired granulopoiesis in severe congenital neutropenia (SCN), we have evaluated bone marrow (BM) stem cell reserve and function and BM stromal cell myelopoiesis supporting capacity in two patients with SCN. METHODS: BM primitive stem cells and myeloid progenitor cells were assessed using flow cytometry, limiting dilution assay, clonogenic assays, and long-term BM cultures (LTBMC). BM stroma function was assessed by evaluating the ability of irradiated stromal layers from the patients to induce granulocyte-macrophage colony formation (CFU-GM) by normal CD34+ cells. RESULTS: Compared to the normal controls (n = 37), SCN patients displayed a low percentage of CD34+/CD38+ cells (P < 0.05), low CFU-GM colony formation by highly purified CD34+ cells (P < 0.05), low CFU-GM recovery in LTBMC (P < 0.05), and normal primitive stem cells as indicated by the frequency of CD34+/CD38- cells and the number of long-term culture initiating cells. Patient BM stromal layers exhibited normal myelopoiesis supporting capacity as shown by the CFU-GM content of irradiated LTBMC recharged with normal CD34+ cells. In addition, patient LTBMC supernatants displayed 20-fold normal granulocyte colony stimulating factor and 2-fold normal granulocyte-macrophage colony stimulating factor levels. CONCLUSION: These data show that primitive BM stem cells and stromal cells are not affected in SCN patients, while they support further the concept of a primary defect at the myeloid progenitor cell level. To know the differentiation stage at which the underlying defect causes the malfunction will be relevant for further elucidation of its nature at the molecular level.

Adult↗

Viral perturbation of endocrine function: disordered cell function leads to disturbed homeostasis and disease.

Virus-induced disease occurs both through direct destruction of cells by viruses and/or secondarily through lysis of infected cells by immunological assault. We asked whether viruses could also cause injury and disease by altering the cell's normal or expected functions without destroying the cells. Here we show that a relatively noncytopathic virus can perturb endocrine functions by disordering the synthesis of a hormone needed for growth and glucose regulation, while replicating in a specialized cell making that hormone. Yet, despite viral replication and alteration in synthesis of the specialized cell's homeostatic product, the infected cell remains free from structural injury.

Animals↗

Functional deficits in basal ganglia of children with attention-deficit/hyperactivity disorder shown with functional magnetic resonance imaging relaxometry.

Attention-deficit/hyperactivity disorder is a highly heritable and prevalent neuropsychiatric disorder estimated to affect 6% of school-age children. Its clinical hallmarks are inattention, hyperactivity and impulsivity, which often respond substantially to treatment with methylphenidate or dextroamphetamine. Etiological theories suggest a deficit in corticostriatal circuits, particularly those components modulated by dopamine. We developed a new functional magnetic resonance imaging procedure (T2 relaxometry) to indirectly assess blood volume in the striatum (caudate and putamen) of boys 6-12 years of age in steady-state conditions. Boys with attention-deficit/hyperactivity disorder had higher T2 relaxation time measures in the putamen bilaterally than healthy control subjects. Relaxation times strongly correlated with the child's capacity to sit still and his accuracy in accomplishing a computerized attention task. Daily treatment with methylphenidate significantly changed the T2 relaxation times in the putamen of children with attention-deficit/hyperactivity disorder, although the magnitude and direction of the effect was strongly dependent on the child's unmedicated activity state. There was a similar but nonsignificant trend in the right caudate. T2 relaxation time measures in thalamus did not differ significantly between groups, and were not affected by methylphenidate. Attention-deficit/hyperactivity disorder symptoms may be closely tied to functional abnormalities in the putamen, which is mainly involved in the regulation of motor behavior.

Attention Deficit Disorder with Hyperactivity↗

Improved lung function tests on changing from topical timolol: non-selective beta-blockade impairs lung function tests in elderly patients.

Fifty-two elderly glaucomatous patients, without a history of asthma or obstructive airways disease, who were using topical timolol for control of intraocular pressure were recruited. Their topical therapy was changed to either betaxolol or pilocarpine. The change was associated with improvement in mean peak flow from 278 l/min to 328 l/min (t = 5.73, p < 0.001), mean FEV1 from 1.66 l to 1.85 l (t = 7.09, p < 0.001) and mean FVC from 2.40 l to 2.64 l (t = 5.07, p < 0.001). Change to either betaxolol or pilocarpine was associated with improved lung function tests. Lung function tests in a control group of 20 showed no significant changes. Both drugs maintained control of intraocular pressure but betaxolol had fewer ocular side effects.

Administration, Topical↗

Axial penile buckling forces vs Rigiscan radial rigidity as a function of intracavernosal pressure: why Rigiscan does not predict functional erections in individual patients.

AIM: An improved understanding of the relationship between radial and axial rigdity values would enable better appreciation of the clinical usefulness of RigiScantrade mark, the most widely utilized determination of erectile rigidity testing. Previous studies have shown that axial rigidity (measured by buckling forces) correlated well with radial rigidity (measured by RigiScantrade mark) for radial rigidity values below 60%. For radial rigidity exceeding 60%, there was poor correlation. Heretofore, there has been no physiologic explanation of this phenomenon. METHODS: During dynamic pharmacocavernosometry in 36 impotent patients, we investigated the relationship between axial buckling forces and RigiScan radial rigidity and, for the first time, how they both vary with pressure, (which we varied over over a wide functional range). In addition, we recorded multiple penile length and diameter values enabling us to relate, also for the first time, axial and radial rigidity to individual mechanical erectile tissue and penile geometric properties. RESULTS: Marked differences were found in the manner RigiScan radial rigidity units and axial buckling force magnitudes increased with increases in intracavernosal pressure values in each individual. The former asymptotically approached a maximum finite value while the latter increased continuously towards infinity. Based on data in this study, RigiScan radial rigidity values greater than 55% may be considered a necessary criteria for vaginal intromission capability in all partners but it is not a sufficient one. CONCLUSIONS: Axial and radial rigidity share a common dependency upon intracavernosal pressure, however, they are also dependent upon other unique physical determinants. For axial rigidity, additional dependent variables include cavernosal erectile tissue properties and penile geometry, while for radial rigidity, this may include tunical surface wall tension properties. Clinical devices which assess functional penile rigidity should utilize axial and not radial rigidity testing.

Equipment Design↗

A transcriptional activation function of p53 is dispensable for and inhibitory of its apoptotic function.

The tumor suppressor p53 is an inducer of cell cycle arrest and programmed cell death (apoptosis). The ability of p53 to induce cell cycle arrest is linked to its ability to induce transcription of genes such as the cyclin-dependent kinase inhibitor p21. However, the dependence of p53-mediated apoptosis on transcriptional activation remains controversial. Ectopic expression of a temperature-sensitive (ts) p53 allele induced expression of p53 target genes and elicited both G1 and G2/M cell cycle arrest upon shift to the permissive temperature. Ectopic expression of the same ts p53 allele with two additional point mutations (Gln22, Ser23) that abolish p53-transcriptional activation did not induce p53 target genes and G1 nor G2/M cell cycle arrest. In HCT116 colon carcinoma cells ectopic expression of wild type p53 does not elicit apoptosis whereas p53 mutant deficient in trans-activation induces apoptosis. The ability of wild type p53 to induce apoptosis is restored in HCT116 cells that are null for p21. However, the trans-activation deficient mutant of p53 is still more potent mediator of apoptosis than wild type p53 in the p21 null cells. Although the ability of Gln22,Ser23 to trans-activate p53 target genes is diminished, it retains the ability to repress Bcl-2 expression. Thus, we conclude that while ectopic expression of wild type p53 can induce both G1 and G2/M arrest, in a p21 dependent manner, without apoptosis, a p53 mutant defective in trans-activation elicits apoptosis without inducing cell cycle arrest. Further, the anti-apoptotic function of p53 is dependent on trans-activation and is linked to cell cycle arrest. The results strongly suggest that the trans-activation deficient mutant is a more potent inducer of apoptosis because it lost its anti-apoptotic function and retains its ability to repress pro-apoptotic genes such as Bcl-2. Taken together, the results imply that employing a trans-activation deficient p53 in gene therapy approaches or the use of drugs that convert mutant p53 to a trans-activation-independent mediator of apoptosis may be much more efficient therapeutic approaches than current approaches that employ wild type p53.

Apoptosis↗

AFM and STM characterization of thiol and thiophene functionalized SWNTs: pitfalls in the use of chemical markers to determine the extent of sidewall functionalization in SWNTs.

Thiol- and thiophene-functionalized SWNTs prepared via the reaction of a substituted amine with fluoronanotubes show similar levels of sidewall functionalization, however, the use of Au nanoparticles as chemical markers for AFM gives misleading results for substituent distribution since STM shows the thiol substituents grouped in bands while the thiophene substituents uniformly distributed along the SWNTs.

Journal Article↗