Location and functional significance of retinol-binding sites on the serine/threonine kinase, c-Raf.

Redox activations of serine/threonine kinases represent alternate pathways in which vitamin A plays a crucial co-factor role. Vitamin A binds the zinc finger domain of c-Raf with nanomolar affinity. The retinoid-binding site has been mapped within this structure by scanning mutagenesis.

Shorter side chains optimize helix-helix packing.

A systematic study of helix-helix packing in a comprehensive database of protein structures revealed that the side chains inside helix-helix interfaces on average are shorter than those in the noninterface parts of the helices. The study follows our earlier study of this effect in transmembrane helices. The results obtained on the entire database of protein structures are consistent with those obtained on the transmembrane helices.

The role of geometric complementarity in secondary structure packing: a systematic docking study.

A strong similarity between the major aspects of protein folding and protein recognition is one of the emerging fundamental principles in protein science. A crucial importance of steric complementarity in protein recognition is a well-established fact. The goal of this study was to assess the importance of the steric complementarity in protein folding, namely, in the packing of the secondary structure elements.

DNA binding is required for the apoptogenic action of apoptosis inducing factor.

The execution of apoptosis or programmed cell death comprises both caspase-dependent and caspase-independent processes. Apoptosis inducing factor (AIF) was identified as a major player in caspase-independent cell death. It induces chromatin condensation and initial DNA cleavage via an unknown molecular mechanism.

Theoretical Study of the Diels-Alder Reaction of Selenoaldehydes and Selenoketones.

The Diels-Alder reaction of a series of substituted selenoaldehydes (Se=CHR; R = H, F, Me, OMe, CH(2)F, CF(3), and CN) or selenoketones (Se=CR(2); R = Me and CN) with 1,3-butadiene or 2-methoxy-1,3-butadiene to yield 3,6-dihydro-2H-selenopyrans were examined using B3LYP with a modified 6-31G basis set. This method is compared with results from a number of standard ab initio procedures and compares well with post-HF results. The Diels-Alder reaction of the selenocarbonyl compounds proceeds through a concerted, though asynchronous, transition state.

Ab Initio Study of the Thio-Ene Reaction. 1. The Enophile Substituent Effect.

The ene reaction between propene and various enophiles (ethene, methanal, methanethial, ethanethial, and cyanomethanethial) were examined at the MP4/6-31G//MP2/6-31G level. The transition structures are all cyclic and concerted. The activation barriers for the thiocarbonyls are significantly lower (ranging from 16.