On the basis of empirical evidence from molecular dynamics simulations, molecular conformational space can be described by means of a partition of central conical regions (cells) characterized by the dominance relations between cartesian coordinates. This work presents a geometric and combinatorial description of the cell arrangement which is polar to a… (More)
For a series of wild type and mutated eucaryotic gene prelude sequences (mainly "promoters" of SV40 early gene (Benoist and Chambon, Nature 290, 304 (1981); Moreau et al., Nuc. Acids Res. 9, 6047 (1982)) and of Herpes Simplex Virus TK gene (McKnight and Kingsbury, Science 217, 316 (1982)), in vivo promoter activity and local stability (denaturability) have… (More)
Realistic 3D-conformations of protein structures can be embedded in a cubic lattice using exclusively integer numbers, additions, subtractions and boolean operations.
Cooperative transitions in DNA (B to Z, B to A, helix to coil, etc.) are known to depend strongly on nucleotide sequence. In general the change in free energy involved in the transition can be expressed as: delta G(seq) = 2RT log (sigma) where sigma is a factor arising from the free energy associated with boundaries of different conformations along the… (More)
The signal qualifying an AUG or GUG as an initiator in mRNAs processed by E. coli ribosomes is not found to be a systematic, literal homology sequence. In contrast, stability analysis reveals that initiators always occur within nucleic acid domains of low stability, for which a high A/U content is observed. Since no aminoacid selection pressure can be… (More)