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Roaming is the dominant mechanism for molecular products in acetaldehyde photodissociation.

ABSTRACT: Reaction pathways that bypass the conventional saddle-point transition state (TS) are of considerable interest and importance. An example of such a pathway, termed "roaming," has been described in the photodissociation of H(2)CO. In a combined experimental and theoretical study, we show that roaming pathways are important in the 308-nm photodissociation of CH(3)CHO to CH(4) + CO. The CH(4) product is found to have extreme vibrational excitation, with the vibrational distribution peaked at approximately 95% of the total available energy. Quasiclassical trajectory calculations on full-dimensional potential energy surfaces reproduce these results and are used to infer that the major route to CH(4) + CO products is via a roaming pathway where a CH(3) fragment abstracts an H from HCO. The conventional saddle-point TS pathway to CH(4) + CO formation plays only a minor role. H-atom roaming is also observed, but this is also a minor pathway. The dominance of the CH(3) roaming mechanism is attributed to the fact that the CH(3) + HCO radical asymptote and the TS saddle-point barrier to CH(4) + CO are nearly isoenergetic. Roaming dynamics are therefore not restricted to small molecules such as H(2)CO, nor are they limited to H atoms being the roaming fragment. The observed dominance of the roaming mechanism over the conventional TS mechanism presents a significant challenge to current reaction rate theory.

SUBMITTER: Heazlewood BR

PROVIDER: S-EPMC2529119 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature

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Roaming is the dominant mechanism for molecular products in acetaldehyde photodissociation.

Heazlewood Brianna R BR Jordan Meredith J T MJ Kable Scott H SH Selby Talitha M TM Osborn David L DL Shepler Benjamin C BC Braams Bastiaan J BJ Bowman Joel M JM

Proceedings of the National Academy of Sciences of the United States of America 20080807 35

Reaction pathways that bypass the conventional saddle-point transition state (TS) are of considerable interest and importance. An example of such a pathway, termed "roaming," has been described in the photodissociation of H(2)CO. In a combined experimental and theoretical study, we show that roaming pathways are important in the 308-nm photodissociation of CH(3)CHO to CH(4) + CO. The CH(4) product is found to have extreme vibrational excitation, with the vibrational distribution peaked at approx ...[more]

PMID: 18687891

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Project description:BackgroundMicrobial lipases represent the most important class of biocatalysts used for a wealth of applications in organic synthesis. An often applied reaction is the lipase-catalyzed transesterification of vinyl esters and alcohols resulting in the formation of acetaldehyde which is known to deactivate microbial lipases, presumably by structural changes caused by initial Schiff-base formation at solvent accessible lysine residues. Previous studies showed that several lipases were sensitive toward acetaldehyde deactivation whereas others were insensitive; however, a general explanation of the acetaldehyde-induced inactivation mechanism is missing.ResultsBased on five microbial lipases from Candida rugosa, Rhizopus oryzae, Pseudomonas fluorescens and Bacillus subtilis we demonstrate that the protonation state of lysine ?-amino groups is decisive for their sensitivity toward acetaldehyde. Analysis of the diverse modification products of Bacillus subtilis lipases in the presence of acetaldehyde revealed several stable products such as ?,?-unsaturated polyenals, which result from base and/or amino acid catalyzed aldol condensation of acetaldehyde. Our studies indicate that these products induce the formation of stable Michael-adducts at solvent-accessible amino acids and thus lead to enzyme deactivation. Further, our results indicate Schiff-base formation with acetaldehyde to be involved in crosslinking of lipase molecules.ConclusionsDifferences in stability observed with various commercially available microbial lipases most probably result from different purification procedures carried out by the respective manufacturers. We observed that the pH of the buffer used prior to lyophilization of the enzyme sample is of utmost importance. The mechanism of acetaldehyde-induced deactivation of microbial lipases involves the generation of ?,?-unsaturated polyenals from acetaldehyde which subsequently form stable Michael-adducts with the enzymes. Lyophilization of the enzymes from buffer at pH 6.0 can provide an easy and effective way to stabilize lipases toward inactivation by acetaldehyde.

Project description:PAX5 encodes a master regulator of B-cell development. It fuses to other genes associated with acute lymphoblastoid leukemia (ALL). These fusion products are potent dominant-negative (DN) inhibitors of wild-type PAX5, resulting in a blockade of B-cell differentiation. Here, we show that multimerization of PAX5 DNA-binding domain (DBD) is necessary and sufficient to cause extremely stable chromatin binding and DN activity. ALL-associated PAX5-C20S results from fusion of the N-terminal region of PAX5, including its paired DBD, to the C-terminus of C20orf112, a protein of unknown function. We report that PAX5-C20S is a tetramer, which interacts extraordinarily stably with chromatin as determined by Fluorescence Recovery After Photobleaching in living cells. Tetramerization, stable chromatin binding and DN activity all require a putative five-turn amphipathic ?-helix at the C-terminus of C20orf112, and does not require potential corepressor binding peptides elsewhere in the sequence. In vitro, the monomeric PAX5 DBD and PAX5-C20S binds a PAX5-binding site with equal affinity when it is at the center of an oligonucleotide too short to bind to more than one PAX5 DBD. But, PAX5-C20S binds the same sequence with 10-fold higher affinity than the monomeric PAX5 DBD when it is in a long DNA molecule. We suggest that the increased affinity results from interactions of one or more of the additional DBDs with neighboring non-specific sites in a long DNA molecule, and that this can account for the increased stability of PAX5-C20S chromatin binding compared with wild-type PAX5, resulting in DN activity by competition for binding to PAX5-target sites. Consistent with this model, the ALL-associated PAX5 fused to ETV6 or the multimerization domain of ETV6 SAM results in stable chromatin binding and DN activity. In addition, PAX5 DBD fused to artificial dimerization, trimerization and tetramerization domains results in parallel increases in the stability of chromatin binding and DN activity. Our studies suggest that oncogenic fusion proteins that retain the DBD of the transcription factor (TF) and the multimerization sequence of the partner protein can act in a DN manner by multimerizing and binding avidly to gene targets, preventing the normal TF from binding and inducing expression of its target genes. Inhibition of this multimeriztion may provide a novel therapeutic approach for cancers with this or similar fusion proteins.

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Roaming is the dominant mechanism for molecular products in acetaldehyde photodissociation.

Publications

Roaming is the dominant mechanism for molecular products in acetaldehyde photodissociation.

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