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81.
Evolution of physics-based methodology for exploring the conformational energy landscape of proteins
Scheraga HA Pillardy J Liwo A Lee J Czaplewski C Ripoll DR Wedemeyer WJ Arnautova YA 《Journal of computational chemistry》2002,23(1):28-34
The evolution of our physics-based computational methods for determining protein conformation without the introduction of secondary-structure predictions, homology modeling, threading, or fragment coupling is described. Initial use of a hard-sphere potential captured much of the structural properties of polypeptide chains, and subsequent more refined force fields, together with efficient methods of global optimization provide indications that progress is being made toward an understanding of the interresidue interactions that underlie protein folding. 相似文献
82.
Becerril HA Stoltenberg RM Wheeler DR Davis RC Harb JN Woolley AT 《Journal of the American Chemical Society》2005,127(9):2828-2829
Three-branched DNA molecules have been designed and assembled from oligonucleotide components. These nucleic acid constructs contain double- and single-stranded regions that control the hybridization behavior of the assembly. Specific localization of a single streptavidin molecule at the center of the DNA complex has been investigated as a model system for the directed placement of nanostructures. Highly selective silver and copper metallization of the DNA template has also been characterized. Specific hybridization of these DNA complexes to oligonucleotide-coupled nanostructures followed by metallization should provide a bottom-up self-assembly route for the fabrication and characterization of discrete three-terminal nanodevices. 相似文献
83.
Photo-extrusion of nitrogen from the azoalkane 1 in the presence of molecular oxygen gave besides the hydrocarbons 3 and 5, the endoperoxide 10 and hydroperoxide 11, the former via trapping of the 1,4-diradical 4 by triplet oxygen, the latter by ene-reaction-6f hydrocarbon 5 with singlet oxygen. 相似文献
84.
Warnick KF Francom SJ Humble PH Kelly RT Woolley AT Lee ML Tolley HD 《Electrophoresis》2005,26(2):405-414
The class of equilibrium gradient methods utilizes the opposition of two forces, at least one of which changes in magnitude with position, to separate and concentrate analytes. The drawback of many methods of this type is that the production of two opposing forces requires in comparison to standard methods, such as capillary electrophoresis, a relatively complex apparatus. In addition, for techniques such as electric field gradient focusing, hydrodynamic flow leads to Taylor dispersion, which limits the attainable concentration factor. We propose a new method, gradient field electrophoresis, which achieves analyte separation and focusing with only one spatially varying force, an electric field gradient. A model for the method is developed and used to analyze peak capacity. Experimental results for a protein (R-phycoerythrin) are given and compared to the model. 相似文献
85.
The 6-hydroperoxy-1,4-cyclooctadiene (), which is formed in the photosensitized oxygenation of 1,5-cyclooctadiene (), affords on further singlet oxygenation 5,8-dihydroperoxy-1,3-cyclooctadiene (), which via triphenylphosphine reduction leads to -5,8-dihydroxy-1,3-cyclooctadiene () and subsequent pyridinium chlorochromate oxidation to 1,3-cyclooctadien-5,8-dione (). 相似文献
86.
Bach RD Dmitrenko O Adam W Schambony S 《Journal of the American Chemical Society》2003,125(4):924-934
Comparative analysis of the calculated gas-phase activation barriers (DeltaE++) for the epoxidation of ethylene with dimethyldioxirane (DMDO) and peroxyformic acid (PFA) [15.2 and 16.4 kcal/mol at QCISD(T)// QCISD/6-31+G(d,p)] and E-2-butene [14.3 and 13.2 kcal/mol at QCISD(T)/6-31G(d)//B3LYP/6-311+G(3df,2p)] suggests similar oxygen atom donor capacities for both oxidants. Competition experiments in CH(2)Cl(2) solvent reveal that DMDO reacts with cyclohexene much faster than peracetic acid/acetic acid under scrupulously dried conditions. The rate of DMDO epoxidation is catalyzed by acetic acid with a reduction in the classical activation barrier of 8 kcal/mol. In many cases, the observed increase in the rate for DMDO epoxidation in solution may be attributed to well-established solvent and hydrogen-bonding effects. This predicted epoxidative reactivity for DMDO is not consistent with what has generally been presumed for a highly strained cyclic peroxide. The strain energy (SE) of DMDO has been reassessed and its moderated value (about 11 kcal/mol) is now more consistent with its inherent gas-phase reactivity toward alkenes in the epoxidation reaction. The unusual thermodynamic stability of DMDO is largely a consequence of the combined geminal dimethyl- and dioxa-substitution effects and unusually strong C-H and C-CH(3) bonds. Methyl(trifluoromethyl)dioxirane (TFDO) exhibits much lower calculated activation barriers than DMDO in the epoxidation reaction (the average DeltaDeltaE++ values are about 7.5 kcal/mol). The rate increase relative to DMDO of approximately 10(5), while consistent with the higher strain energy for TFDO (SE approximately 19 kcal/mol) is attributed largely to the inductive effect of the CF(3) group. We have also examined the effect of alkene strain on the rate of epoxidation with PFA. The epoxidation barriers are only slightly higher for the strained alkenes cyclopropene (DeltaE++ = 14.5 kcal/mol) and cyclobutene (DeltaE++ = 13.7 kcal/mol) than for cyclopentene (DeltaE++ = 12.1 kcal/mol), reflecting the fact there is little relief of strain in the transition state. Alkenes strained by twist or pi-bond torsion do exhibit much lower activation barriers. 相似文献
87.
Tao Huang Seyyedmohsen Hosseinibarkooie Adam L. Borne Mitchell E. Granade Jeffrey W. Brulet Thurl E. Harris Heather A. Ferris Ku-Lung Hsu 《Chemical science》2021,12(9):3295
Sulfonyl-triazoles are a new class of electrophiles that mediate covalent reaction with tyrosine residues on proteins through sulfur-triazole exchange (SuTEx) chemistry. Recent studies demonstrate the broad utility and tunability of SuTEx chemistry for chemical proteomics and protein ligand discovery. Here, we present a strategy for mapping protein interaction networks of structurally complex binding elements using functionalized SuTEx probes. We show that the triazole leaving group (LG) can serve as a releasable linker for embedding hydrophobic fragments to direct molecular recognition while permitting efficient proteome-wide identification of binding sites in live cells. We synthesized a series of SuTEx probes functionalized with a lipid kinase fragment binder for discovery of ligandable tyrosines residing in catalytic and regulatory domains of protein and metabolic kinases in live cells. We performed competition studies with kinase inhibitors and substrates to demonstrate that probe binding is occurring in an activity-dependent manner. Our functional studies led to discovery of probe-modified sites within the C2 domain that were important for downregulation of protein kinase C-alpha in response to phorbol ester activation. Our proof of concept studies highlight the triazole LG of SuTEx probes as a traceless linker for locating protein binding sites targeted by complex recognition elements in live cells.Sulfonyl-triazole probes modified with a kinase recognition element are developed for live cell activity-based profiling to identify tyrosine sites located in catalytic and regulatory domains that are important for kinase function. 相似文献
88.
Andrzej Maączyński Marian Góral Barbara Wiśniewska-Gocłowska Adam Skrzecz David Shaw 《Monatshefte für Chemie / Chemical Monthly》2003,134(5):633-653
Summary. The evaluation of mutual solubility data for systems water with n-alkanes, isoalkanes, and cycloalkanes along the three phase line is reported and a formula for the prediction of solubility
of alkanes in water is developed. Then a cubic equation of state with an added term, which accounts for hydrogen bonding is
used for correlation of liquid–liquid equilibrium data and for prediction of solubility of water in hydrocarbons using alkane
in water solubility data. Comparison of the predicted and experimental solubilities is performed using all accessible experimental
data. With this approach it is possible to predict the solubilities of water in alkanes with good accuracy over the temperature
range up to about 20 K below critical temperature. Solubility of alkanes in water can also be calculated using experimental
data for solubility of water in alkanes but results of these calculations are more sensitive to experimental errors of the
data.
Corresponding author: E-mail: macz@ichf.edu.pl
Received August 5, 2002; accepted (revised) September 13, 2002
Published online March 13, 2003
RID="a"
ID="a" Dedicated to Prof. Dr. H. Gamsj?ger on the occasion of his 70th birthday anniversary 相似文献
89.
Adam S. Paziak Lech Celewicz Krzysztof Ciszewski Krzysztof Golankiewicz 《Journal of mass spectrometry : JMS》1993,28(5):643-646
The electron impact mass spectra of 6-methyltetrazolo[1,5-c]pyrimidin-5(6H)-one, its 7- and 8-methyl derivatives, three 8-halo derivatives and two related nucleosides are reported. On the basis of the high-resolution data and detected metastable ions, the fragmentation routes of their molecular ions are proposed. Coexistence of the tautomeric forms of the title compounds of cyclic (tetrazole) or linear (azide) structure can be suggested owing to the fragmentation pathways identified for the bases. Decomposition of the related nucleosides lies in the breaking of nucleoside bonds to produce the appropriate base and sugar fragments. 相似文献
90.
A series of trialkylsilyl esters were deprotected or transesterificated into their corresponding carboxylic acids or methyl esters under a catalytic amount of CBr4 in alcohol reaction system. This method enables to desilylate secondary sp3-carbon, sp2-carbon, sp-carbon and aryl tethered trialkylsilyl esters to carboxylic acids, whereas primary sp3-carbon tethered trialkylsilyl esters were further converted into their methyl esters under CBr4/MeOH reaction conditions. The highly chemoselective deprotections can be modulated and achieved by the introduced protecting trialkylsilyl groups and the used alcohols such as MeOH and EtOH under this photochemically-induced reaction conditions. 相似文献