3,065 research outputs found
Unifying thermodynamic and kinetic descriptions of single-molecule processes: RNA unfolding under tension
We use mesoscopic non-equilibrium thermodynamics theory to describe RNA
unfolding under tension. The theory introduces reaction coordinates,
characterizing a continuum of states for each bond in the molecule. The
unfolding considered is so slow that one can assume local equilibrium in the
space of the reaction coordinates. In the quasi-stationary limit of high
sequential barriers, our theory yields the master equation of a recently
proposed sequential-step model. Non-linear switching kinetics is found between
open and closed states. Our theory unifies the thermodynamic and kinetic
descriptions and offers a systematic procedure to characterize the dynamics of
the unfolding processComment: 13 pages, 3 figure
Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding
Ribosome is a molecular machine that polymerizes a protein where the sequence
of the amino acid residues, the monomers of the protein, is dictated by the
sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that
serves as the template. The ribosome is a molecular motor that utilizes the
template mRNA strand also as the track. Thus, in each step the ribosome moves
forward by one codon and, simultaneously, elongates the protein by one amino
acid. We present a theoretical model that captures most of the main steps in
the mechano-chemical cycle of a ribosome. The stochastic movement of the
ribosome consists of an alternating sequence of pause and translocation; the
sum of the durations of a pause and the following translocation is the time of
dwell of the ribosome at the corresponding codon. We derive the analytical
expression for the distribution of the dwell times of a ribosome in our model.
Whereever experimental data are available, our theoretical predictions are
consistent with those results. We suggest appropriate experiments to test the
new predictions of our model, particularly, the effects of the quality control
mechanism of the ribosome and that of their crowding on the mRNA track.Comment: This is an author-created, un-copyedited version of an article
accepted for publication in Physical Biology. IOP Publishing Ltd is not
responsible for any errors or omissions in this version of the manuscript or
any version derived from it. The definitive publisher authenticated version
is available online at DOI:10.1088/1478-3975/8/2/02600
Probing protein sequences as sources for encrypted antimicrobial peptides
Starting from the premise that a wealth of potentially biologically active peptides may lurk within proteins, we describe here a methodology to identify putative antimicrobial peptides encrypted in protein sequences. Candidate peptides were identified using a new screening procedure based on physicochemical criteria to reveal matching peptides within protein databases. Fifteen such peptides, along with a range of natural antimicrobial peptides, were examined using DSC and CD to characterize their interaction with phospholipid membranes. Principal component analysis of DSC data shows that the investigated peptides group according to their effects on the main phase transition of phospholipid vesicles, and that these effects correlate both to antimicrobial activity and to the changes in peptide secondary structure. Consequently, we have been able to identify novel antimicrobial peptides from larger proteins not hitherto associated with such activity, mimicking endogenous and/or exogenous microorganism enzymatic processing of parent proteins to smaller bioactive molecules. A biotechnological application for this methodology is explored. Soybean (Glycine max) plants, transformed to include a putative antimicrobial protein fragment encoded in its own genome were tested for tolerance against Phakopsora pachyrhizi, the causative agent of the Asian soybean rust. This procedure may represent an inventive alternative to the transgenic technology, since the genetic material to be used belongs to the host organism and not to exogenous sources
Host-induced gene silencing in the necrotrophic fungal pathogen Sclerotinia sclerotiorum.
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