177 research outputs found
DNA-condensation, redissolution and mesocrystals induced by tetravalent counterions
The distance-resolved effective interaction potential between two parallel
DNA molecules is calculated by computer simulations with explicit tetravalent
counterions and monovalent salt. Adding counterions first yields an attractive
minimum in the potential at short distances which then disappears in favor of a
shallower minimum at larger separations. The resulting phase diagram includes a
DNA-condensation and redissolution transition and a stable mesocrystal with an
intermediate lattice constant for high counterion concentration.Comment: 4 pages, 4 figure
DNA delivery by phage as a strategy for encapsulating toroidal condensates of arbitrary size into liposomes
DNA condensation and redissolution: Interaction between overcharged DNA molecules
The effective DNA-DNA interaction force is calculated by computer simulations
with explicit tetravalent counterions and monovalent salt. For overcharged DNA
molecules, the interaction force shows a double-minimum structure. The
positions and depths of these minima are regulated by the counterion density in
the bulk. Using two-dimensional lattice sum and free energy perturbation
theories, the coexisting phases for DNA bundles are calculated. A
DNA-condensation and redissolution transition and a stable mesocrystal with an
intermediate lattice constant for high counterion concentration are obtained.Comment: 26 pages, 10 figure
Phase diagram of aggregation of oppositely charged colloids in salty water
Aggregation of two oppositely charged colloids in salty water is studied. We
focus on the role of Coulomb interaction in strongly asymmetric systems in
which the charge and size of one colloid is much larger than the other one. In
the solution, each large colloid (macroion) attracts certain number of
oppositely charged small colloids (-ion) to form a complex. If the
concentration ratio of the two colloids is such that complexes are not strongly
charged, they condense in a macroscopic aggregate. As a result, the phase
diagram in a plane of concentrations of two colloids consists of an aggregation
domain sandwiched between two domains of stable solutions of complexes. The
aggregation domain has a central part of total aggregation and two wings
corresponding to partial aggregation. A quantitative theory of the phase
diagram in the presence of monovalent salt is developed. It is shown that as
the Debye-H\"{u}ckel screening radius decreases, the aggregation domain
grows, but the relative size of the partial aggregation domains becomes much
smaller. As an important application of the theory, we consider solutions of
long double-helix DNA with strongly charged positive spheres (artificial
chromatin). We also consider implications of our theory for in vitro
experiments with the natural chromatin. Finally, the effect of different shapes
of macroions on the phase diagram is discussed.Comment: 10 pages, 9 figures. The text is rewritten, but results are not
change
Conformational Instability of Rodlike Polyelectrolytes due to Counterion Fluctuations
The effective elasticity of highly charged stiff polyelectrolytes is studied
in the presence of counterions, with and without added salt. The rigid polymer
conformations may become unstable due to an effective attraction induced by
counterion density fluctuations. Instabilities at the longest, or intermediate
length scales may signal collapse to globule, or necklace states, respectively.
In the presence of added-salt, a generalized electrostatic persistence length
is obtained, which has a nontrivial dependence on the Debye screening length.
It is also found that the onset of conformational instability is a re-entrant
phenomenon as a function of polyelectrolyte length for the unscreened case, and
the Debye length or salt concentration for the screened case. This may be
relevant in understanding the experimentally observed re-entrant condensation
of DNA.Comment: 8 pages, 4 figure
Phase Behavior of Columnar DNA Assemblies
The pair interaction between two stiff parallel linear DNA molecules depends
not only on the distance between their axes but on their azimuthal orientation.
The positional and orientational order in columnar B-DNA assemblies in solution
is investigated, based on the DNA-DNA electrostatic pair potential that takes
into account DNA helical symmetry and the amount and distribution of adsorbed
counterions. A phase diagram obtained by lattice sum calculations predicts a
variety of positionally and azimuthally ordered phases and bundling transitions
strongly depending on the counterion adsorption patterns.Comment: 4 pages, 3 figures, submitted to PR
NMR investigations of the interaction between the azo-dye sunset yellow and Fluorophenol
The interaction of small molecules with larger noncovalent assemblies is important across a wide range of disciplines. Here, we apply two complementary NMR spectroscopic methods to investigate the interaction of various fluorophenol isomers with sunset yellow. This latter molecule is known to form noncovalent aggregates in isotropic solution, and form liquid crystals at high concentrations. We utilize the unique fluorine-19 nucleus of the fluorophenol as a reporter of the interactions via changes in both the observed chemical shift and diffusion coefficients. The data are interpreted in terms of the indefinite self-association model and simple modifications for the incorporation of a second species into an assembly. A change in association mode is tentatively assigned whereby the fluorophenol binds end-on with the sunset yellow aggregates at low concentration and inserts into the stacks at higher concentrations
The Persistence Length of a Strongly Charged, Rod-like, Polyelectrolyte in the Presence of Salt
The persistence length of a single, intrinsically rigid polyelectrolyte
chain, above the Manning condensation threshold is investigated theoretically
in presence of added salt. Using a loop expansion method, the partition
function is consistently calculated, taking into account corrections to
mean-field theory. Within a mean-field approximation, the well-known results of
Odijk, Skolnick and Fixman are reproduced. Beyond mean-field, it is found that
density correlations between counterions and thermal fluctuations reduce the
stiffness of the chain, indicating an effective attraction between monomers for
highly charged chains and multivalent counterions. This attraction results in a
possible mechanical instability (collapse), alluding to the phenomenon of DNA
condensation. In addition, we find that more counterions condense on slightly
bent conformations of the chain than predicted by the Manning model for the
case of an infinite cylinder. Finally, our results are compared with previous
models and experiments.Comment: 13 pages, 2 ps figure
A simple and fast heuristic for protein structure comparison
Background
Protein structure comparison is a key problem in bioinformatics. There exist several methods for doing protein comparison, being the solution of the Maximum Contact Map Overlap problem (MAX-CMO) one of the alternatives available. Although this problem may be solved using exact algorithms, researchers require approximate algorithms that obtain good quality solutions using less computational resources than the formers.
Results
We propose a variable neighborhood search metaheuristic for solving MAX-CMO. We analyze this strategy in two aspects: 1) from an optimization point of view the strategy is tested on two different datasets, obtaining an error of 3.5%(over 2702 pairs) and 1.7% (over 161 pairs) with respect to optimal values; thus leading to high accurate solutions in a simpler and less expensive way than exact algorithms; 2) in terms of protein structure classification, we conduct experiments on three datasets and show that is feasible to detect structural similarities at SCOP's family and CATH's architecture levels using normalized overlap values. Some limitations and the role of normalization are outlined for doing classification at SCOP's fold level.
Conclusion
We designed, implemented and tested.a new tool for solving MAX-CMO, based on a well-known metaheuristic technique. The good balance between solution's quality and computational effort makes it a valuable tool. Moreover, to the best of our knowledge, this is the first time the MAX-CMO measure is tested at SCOP's fold and CATH's architecture levels with encouraging results.
Software is available for download at http://modo.ugr.es/jrgonzalez/msvns4maxcmo webcite.This work is supported by Projects HeuriCosc TIN2005-08404-C04-01, HeuriCode TIN2005-08404-C04-03, both from the Spanish Ministry of Education and Science.
JRG acknowledges financial support from Project TIC2002-04242-C03-02.
Authors thank N. Krasnogor and ProCKSi project (BB/C511764/1) for their support
Clinical Outcomes with and without Adherence to Evidence-Based Medicine Guidelines for Lumbar Degenerative Spondylolisthesis Fusion Patients
Introduction: Degenerative lumbar spondylolisthesis (DS) patients are treated with instrumented fusion, following EBM guidelines, and typically have excellent clinical outcomes. However, not all lumbar fusion procedures adhere to EBM guidelines, typically due to a lack of prospective data.
Objective: This retrospective study compared outcomes of DS lumbar fusion patients treated according to EBM guidelines (EBM concordant) to lumbar fused patients with procedures that did not have clear EBM literature that supported this treatment, the goal being to examine the value of present EBM to guide clinical care.
Methods: A total of 125 DS patients were considered EBM concordant, while 21 patients were EBM discordant. Pre- and postsurgical ODI scores were collected. Clinical outcomes were stratified into substantial clinical benefit (SCB ΔODI \u3e10 points), minimal clinical importance benefit (MCID ΔODI ≥ 5 points), no MCID (ΔODI \u3c 5 points), and a group that showed no change or worsening ODI. Fisher\u27s exact and χ2 tests for categorical variables, Student\u27s t-test for continuous variables, and descriptive statistics were used. Statistical tests were computed at the 95% level of confidence.
Results: Analysis of 125 degenerative spondylolisthesis patients was performed comparing preoperative and postoperative (6 months) ODI scores. ODI improved by 8 points in the EBM concordant group vs. 2.1 points in the EBM discordant group (p = 0.002). Compliance with EBM guidelines was associated with an odds ratio (OR) of 2.93 for achieving MCID ([CI]: 1.12-7.58, p = 0.027).
Conclusions: Patients whose lumbar fusions met EBM criteria had better self-reported outcomes at six months than those who did not meet the requirements. A greater knowledge set is needed to help further support EBM-guided patient care
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