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101.
102.
Combining protein evolution and secondary structure 总被引:10,自引:9,他引:10
An evolutionary model that combines protein secondary structure and amino
acid replacement is introduced. It allows likelihood analysis of aligned
protein sequences and does not require the underlying secondary (or
tertiary) structures of these sequences to be known. One component of the
model describes the organization of secondary structure along a protein
sequence and another specifies the evolutionary process for each category
of secondary structure. A database of proteins with known secondary
structures is used to estimate model parameters representing these two
components. Phylogeny, the third component of the model, can be estimated
from the data set of interest. As an example, we employ our model to
analyze a set of sucrose synthase sequences. For the evolution of sucrose
synthase, a parametric bootstrap approach indicates that our model is
statistically preferable to one that ignores secondary structure.
相似文献
103.
104.
Krishanu Mukherjee Everly Conway de Macario Alberto JL Macario Luciano Brocchieri 《BMC evolutionary biology》2010,10(1):64
Background
Chaperonin proteins are well known for the critical role they play in protein folding and in disease. However, the recent identification of three diverged chaperonin paralogs associated with the human Bardet-Biedl and McKusick-Kaufman Syndromes (BBS and MKKS, respectively) indicates that the eukaryotic chaperonin-gene family is larger and more differentiated than previously thought. The availability of complete genome sequences makes possible a definitive characterization of the complete set of chaperonin sequences in human and other species. 相似文献105.
106.
107.
108.
Marija Cvijović Daniel Dalevi Elizabeth Bilsland Graham JL Kemp Per Sunnerhagen 《BMC bioinformatics》2007,8(1):295
Background
The translational efficiency of an mRNA can be modulated by upstream open reading frames (uORFs) present in certain genes. A uORF can attenuate translation of the main ORF by interfering with translational reinitiation at the main start codon. uORFs also occur by chance in the genome, in which case they do not have a regulatory role. Since the sequence determinants for functional uORFs are not understood, it is difficult to discriminate functional from spurious uORFs by sequence analysis. 相似文献109.
110.
Experiments have explored the possible relationships between the flagellar surface motility of chlamydomonas, visualized as translocation of polystyrene beads by paralyzed (pf) mutants (Bloodgood, 1977, J. Cell Biol. 15:983-989), and the capacity of gametic flagella to participate in the mating reaction. While vegetative and gametic flagella bind beads with equal efficiencies and are capable of transporting them along entire flagellar lengths, beads on vegetative flagella are primarily associated with the proximal half of the flagella whereas those of gametic flagella exhibit no such preference. This difference may relate to the "tipping" response of gametes during sexual flagellar agglutination (Goodenough and Jurivich, 1978, J. Cell Biol. 79:680-693). Colchicine, vinblastine, chymotrypsin, cytochalasins B and D, and anti-β-tubulin antiserum are all able to inhibit the binding of beads to the flagellar suface. Trysin digestion and an antiserum directed against whole chlamydomonas flagella have no effect on the ability of flagella to bind beads, but the beads remain immobile. These results suggest that at least two flagellar activities participate in surface motility: (a) bead binding, which may involve a tubulin-like component at the flagellar surface; and (b) bead translocation, which may depend on a second component (e.g. an ATPase) of the flagellar surface. Surface motility is shown to be distinct from gametic adhesiveness per se, but it may participate in concentrating dispersed agglutinins, in driving them toward the flagellar tips, and/or in generating a signal-to-fuse from the flagellar tips to the cell body. Directly supporting these concepts is the observation that bound beads remain immobilized at the flagellar tips during the "tip-locking" stage of pf x pf matings, and the observation that bound ligands such as antibody fail to be tipped by trypsinized flagella. 相似文献