41 research outputs found
Using of high-speed mills for biomass disintegration
ArticleThe need for mechanical disintegration of biomass is very current topic with regard to
the requirements of an agrarian sector, beside the importance of a materialâs moisture content
reduction to be used in further applications. The drawbacks of commonly applied devices are the
limited use of moist biomass and high energy consumption for disintegration. In collaboration
with LAVARIS company, there were tested two high-speed mills LAV 400/1R with single rotor
(used for a first milling) and LAV 300/2R with double rotors (used for a second milling), which
were primarily designed for crushing of concrete, rubber and construction waste. The goal of the
new technical solution was a disintegration of biomass on example of pine sawdust and
miscanthus together with examination of simultaneous drying in order to achieve a desired
fraction (particle size) and moisture content of biomass material. Experimental tests on highspeed mills have shown the following results: in case of pine sawdust about 98% of output particle
size after passing through the first and second milling was smaller than 1.5 mm, and smaller than
1 mm for miscanthus (sieve analysis method was used for determination), i.e. significant
reduction was achieved comparing to initial particle size. Moisture content of the materials after
disintegration (first and second) decreased from 37.08% to 8.55% for pine sawdust and from
24.43% to 7.19% for miscanthus. Based on the results, it can be concluded that the mechanical
disintegration of biomass by high-speed mills has a great potential to become an effective part of
raw materialsâ pre-treatment technology, not only in agriculture, but also in production of
different types of biofuels
Extended molecular dynamics of a c-kit promoter quadruplex.
The 22-mer c-kit promoter sequence folds into a parallel-stranded quadruplex with a unique structure, which has been elucidated by crystallographic and NMR methods and shows a high degree of structural conservation. We have carried out a series of extended (up to 10 ÎŒs long, âŒ50 ÎŒs in total) molecular dynamics simulations to explore conformational stability and loop dynamics of this quadruplex. Unfolding no-salt simulations are consistent with a multi-pathway model of quadruplex folding and identify the single-nucleotide propeller loops as the most fragile part of the quadruplex. Thus, formation of propeller loops represents a peculiar atomistic aspect of quadruplex folding. Unbiased simulations reveal ÎŒs-scale transitions in the loops, which emphasizes the need for extended simulations in studies of quadruplex loops. We identify ion binding in the loops which may contribute to quadruplex stability. The long lateral-propeller loop is internally very stable but extensively fluctuates as a rigid entity. It creates a size-adaptable cleft between the loop and the stem, which can facilitate ligand binding. The stability gain by forming the internal network of GA base pairs and stacks of this loop may be dictating which of the many possible quadruplex topologies is observed in the ground state by this promoter quadruplex
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field
Structural diversity of supercoiled DNA
By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with
biochemical analyses to investigate structures of individual purified DNA min icircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle
torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and
provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function
Structural Dynamics of Lateral and Diagonal Loops of Human Telomeric G-Quadruplexes in Extended MD Simulations
The NMR solution structures of human telomeric (Htel) G-quadruplexes (GQs) are characterized by the presence of two lateral loops complemented by either diagonal or propeller loops. Bases of a given loop can establish interactions within the loop as well as with other loops and the flanking bases. This can lead to a formation of base alignments above and below the GQ stems. These base alignments are known to affect the loop structures and relative stabilities of different Htel GQ folds. We have carried out a total of 217 ÎŒs of classical (unbiased) molecular dynamics (MD) simulations starting from the available solution structures of Htel GQs to characterize structural dynamics of the lateral and diagonal loops, using several recent AMBER DNA force-field variants. As the loops are involved in diverse stacking and H-bonding interactions, their dynamics is slow, and extended sampling is required to capture different conformations. Nevertheless, although the simulations are far from being quantitatively converged, the data suggest that multiple 10 ÎŒs-scale simulations can provide a quite good assessment of the loop conformational space as described by the force field. The simulations indicate that the lateral loops may sample multiple coexisting conformations, which should be considered when comparing simulations with the NMR models as the latter include ensemble averaging. The adenineâthymine WatsonâCrick arrangement was the most stable base pairing in the simulations. Adenineâadenine and thymineâthymine base pairs were also sampled but were less stable. The data suggest that the description of lateral and diagonal GQ loops in contemporary MD simulations is considerably more realistic than the description of propeller loops, though definitely not flawless
RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution
Can We Execute Stable Microsecond-Scale Atomistic Simulations of ProteinâRNA Complexes?
We
report over 30 ÎŒs of unrestrained molecular dynamics simulations
of six proteinâRNA complexes in explicit solvent. We utilize
the AMBER ff99bsc0Ï<sub>OL3</sub> RNA force field combined with
the ff99SB protein force field and its more recent ff12SB version
with reparametrized side-chain dihedrals. The simulations show variable
behavior, ranging from systems that are essentially stable to systems
with progressive deviations from the experimental structure, which
we could not stabilize anywhere close to the starting experimental
structure. For some systems, microsecond-scale simulations are necessary
to achieve stabilization after initial sizable structural perturbations.
The results show that simulations of proteinâRNA complexes
are challenging and every system should be treated individually. The
simulations are affected by numerous factors, including properties
of the starting structures (the initially high force field potential
energy, resolution limits, conformational averaging, crystal packing,
etc.), force field imbalances, and real flexibility of the studied
systems. These factors, and thus the simulation behavior, differ from
system to system. The structural stability of simulated systems does
not correlate with the size of buried interaction surface or experimentally
determined binding affinities but reflects the type of proteinâRNA
recognition. ProteinâRNA interfaces involving shape-specific
recognition of RNA are more stable than those relying on sequence-specific
RNA recognition. The differences between the protein force fields
are considerably smaller than the uncertainties caused by sampling
and starting structures. The ff12SB improves description of the tyrosine
side-chain group, which eliminates some problems associated with tyrosine
dynamics
Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM
Human antigen R (HuR) is a key regulator of cellular mRNAs containing adenylate/uridylateârich elements (AU-rich elements; AREs). These are a major class of cis elements within 3âČ untranslated regions, targeting these mRNAs for rapid degradation. HuR contains three RNA recognition motifs (RRMs): a tandem RRM1 and 2, followed by a flexible linker and a C-terminal RRM3. While RRM1 and 2 are structurally characterized, little is known about RRM3. Here we present a 1.9-Ă
-resolution crystal structure of RRM3 bound to different ARE motifs. This structure together with biophysical methods and cell-culture assays revealed the mechanism of RRM3 ARE recognition and dimerization. While multiple RNA motifs can be bound, recognition of the canonical AUUUA pentameric motif is possible by binding to two registers. Additionally, RRM3 forms homodimers to increase its RNA binding affinity. Finally, although HuR stabilizes ARE-containing RNAs, we found that RRM3 counteracts this effect, as shown in a cell-based ARE reporter assay and by qPCR with native HuR mRNA targets containing multiple AUUUA motifs, possibly by competing with RRM12.ISSN:0027-8424ISSN:1091-649