31 research outputs found
Capturing the essence of folding and functions of biomolecules using Coarse-Grained Models
The distances over which biological molecules and their complexes can
function range from a few nanometres, in the case of folded structures, to
millimetres, for example during chromosome organization. Describing phenomena
that cover such diverse length, and also time scales, requires models that
capture the underlying physics for the particular length scale of interest.
Theoretical ideas, in particular, concepts from polymer physics, have guided
the development of coarse-grained models to study folding of DNA, RNA, and
proteins. More recently, such models and their variants have been applied to
the functions of biological nanomachines. Simulations using coarse-grained
models are now poised to address a wide range of problems in biology.Comment: 37 pages, 8 figure
Cold-adaptation in sea-water-borne signal proteins: sequence and NMR structure of the pheromone En-6 from antarctic ciliate Euplotes nobilii
Ciliates of Euplotes species constitutively secrete pleiotropic protein pheromones, which are capable to function as prototypic autocrine growth factors as well as paracrine inducers of mating processes. This paper reports
the amino acid sequence and the NMR structure of the pheromone En-6 isolated from the antarctic species Euplotes nobilii. The 63-residue En-6 polypeptide chain forms three α-helices in positions 18–25, 36–40 and 46–56, which are arranged in an up-down-up three-helix bundle forming the edges of a distorted trigonal pyramid. The base of the pyramid is covered by the N-terminal heptadecapeptide segment, which includes a 310-turn of residues 3–6. This topology is covalently anchored by four long-range disulfide bonds. Comparison with the smaller pheromones of E. raikovi, a closely related species living in temperate waters, shows that the twopheromone families have the same three-helix bundle architecture. It then appears that cold-adaptation of the En proteins is primarily related to increased lengths of the chain-terminal peptide segments and the surfaceexposed
loops connecting the regular secondary structures, and to the
presence of solvent-exposed clusters of negatively charged side-chains
RNA Post-transcriptional Modifications of an Early-Stage Large-Subunit Ribosomal Intermediate
Protein
production by ribosomes is fundamental to life, and proper
assembly of the ribosome is required for protein production. The RNA,
which is post-transcriptionally modified, provides the platform for
ribosome assembly. Thus, a complete understanding of ribosome assembly
requires the determination of the RNA post-transcriptional modifications
in all of the ribosome assembly intermediates and on each pathway.
There are 26 RNA post-transcriptional modifications in 23S RNA of
the mature Escherichia coli (E. coli) large ribosomal subunit. The levels of these
modifications have been investigated extensively only for a small
number of large subunit intermediates and under a limited number of
cellular and environmental conditions. In this study, we determined
the level of incorporations of 2-methyl adenosine, 3-methyl pseudouridine,
5-hydroxycytosine, and seven pseudouridines in an early-stage E. coli large-subunit assembly intermediate with
a sedimentation coefficient of 27S. The 27S intermediate is one of
three large subunit intermediates accumulated in E.
coli cells lacking the DEAD-box RNA helicase DbpA
and expressing the helicase inactive R331A DbpA construct. The majority
of the investigated modifications are incorporated into the 27S large
subunit intermediate to similar levels to those in the mature 50S
large subunit, indicating that these early modifications or the enzymes
that incorporate them play important roles in the initial events of
large subunit ribosome assembly