163 research outputs found
Sterols sense swelling in lipid bilayers
In the mimetic membrane system of phosphatidylcholine bilayers, thickening
(pre-critical behavior, anomalous swelling) of the bilayers is observed, in the
vicinity of the main transition, which is non-linear with temperature. The
sterols cholesterol and androsten are used as sensors in a time-resolved
simultaneous small- and wide angle x-ray diffraction study to investigate the
cause of the thickening. We observe precritical behavior in the pure lipid
system, as well as with sterol concentrations less than 15%. To describe the
precritical behavior we introduce a theory of precritical phenomena.The good
temperature resolution of the data shows that a theory of the influence of
fluctuations needs modification. The main cause of the critical behavior
appears to be a changing hydration of the bilayer.Comment: 11 pages, 7 ps figures included, to appear in Phys.Rev.
The influence of anesthetics, neurotransmitters and antibiotics on the relaxation processes in lipid membranes
In the proximity of melting transitions of artificial and biological
membranes fluctuations in enthalpy, area, volume and concentration are
enhanced. This results in domain formation, changes of the elastic constants,
changes in permeability and slowing down of relaxation processes. In this study
we used pressure perturbation calorimetry to investigate the relaxation time
scale after a jump into the melting transition regime of artificial lipid
membranes. This time corresponds to the characteristic rate of domain growth.
The studies were performed on single-component large unilamellar and
multilamellar vesicle systems with and without the addition of small molecules
such as general anesthetics, neurotransmitters and antibiotics. These drugs
interact with membranes and affect melting points and profiles. In all systems
we found that heat capacity and relaxation times are related to each other in a
simple manner. The maximum relaxation time depends on the cooperativity of the
heat capacity profile and decreases with a broadening of the transition. For
this reason the influence of a drug on the time scale of domain formation
processes can be understood on the basis of their influence on the heat
capacity profile. This allows estimations of the time scale of domain formation
processes in biological membranes.Comment: 12 pages, 6 figure
IgTM: An algorithm to predict transmembrane domains and topology in proteins
<p>Abstract</p> <p>Background</p> <p>Due to their role of receptors or transporters, membrane proteins play a key role in many important biological functions. In our work we used Grammatical Inference (GI) to localize transmembrane segments. Our GI process is based specifically on the inference of Even Linear Languages.</p> <p>Results</p> <p>We obtained values close to 80% in both specificity and sensitivity. Six datasets have been used for the experiments, considering different encodings for the input sequences. An encoding that includes the topology changes in the sequence (from inside and outside the membrane to it and vice versa) allowed us to obtain the best results. This software is publicly available at: <url>http://www.dsic.upv.es/users/tlcc/bio/bio.html</url></p> <p>Conclusion</p> <p>We compared our results with other well-known methods, that obtain a slightly better precision. However, this work shows that it is possible to apply Grammatical Inference techniques in an effective way to bioinformatics problems.</p
Identification of Membrane Proteins in the Hyperthermophilic Archaeon Pyrococcus Furiosus Using Proteomics and Prediction Programs
Cell-free extracts from the hyperthermophilic archaeon Pyrococcus furiosus were
separated into membrane and cytoplasmic fractions and each was analyzed by 2D-gel
electrophoresis. A total of 66 proteins were identified, 32 in the membrane fraction and 34
in the cytoplasmic fraction. Six prediction programs were used to predict the subcellular
locations of these proteins. Three were based on signal-peptides (SignalP, TargetP, and
SOSUISignal) and three on transmembrane-spanning α-helices (TSEG, SOSUI, and
PRED-TMR2). A consensus of the six programs predicted that 23 of the 32 proteins
(72%) from the membrane fraction should be in the membrane and that all of the proteins
from the cytoplasmic fraction should be in the cytoplasm. Two membrane-associated
proteins predicted to be cytoplasmic by the programs are also predicted to consist
primarily of transmembrane-spanning β-sheets using porin protein models, suggesting that
they are, in fact, membrane components. An ATPase subunit homolog found in the
membrane fraction, although predicted to be cytoplasmic, is most likely complexed with
other ATPase subunits in the membrane fraction. An additional three proteins predicted to
be cytoplasmic but found in the membrane fraction, may be cytoplasmic contaminants.
These include a chaperone homolog that may have attached to denatured membrane
proteins during cell fractionation. Omitting these three proteins would boost the
membrane-protein predictability of the models to near 80%. A consensus prediction using
all six programs for all 2242 ORFs in the P. furiosus genome estimates that 24% of the
ORF products are found in the membrane. However, this is likely to be a minimum value
due to the programs’ inability to recognize certain membrane-related proteins, such as
subunits associated with membrane complexes and porin-type proteins
Computational Comparative Study of Tuberculosis Proteomes Using a Model Learned from Signal Peptide Structures
Secretome analysis is important in pathogen studies. A fundamental and convenient way to identify secreted proteins is to first predict signal peptides, which are essential for protein secretion. However, signal peptides are highly complex functional sequences that are easily confused with transmembrane domains. Such confusion would obviously affect the discovery of secreted proteins. Transmembrane proteins are important drug targets, but very few transmembrane protein structures have been determined experimentally; hence, prediction of the structures is essential. In the field of structure prediction, researchers do not make assumptions about organisms, so there is a need for a general signal peptide predictor
50 years of amino acid hydrophobicity scales: revisiting the capacity for peptide classification
On the anomalous viscosity of monodisperse latex in the disordered state
It is found that the viscosity of a monodisperse polystyrene latex in the disordered state increases anomalously when the disorder-order transition point is approached. This anomalous behaviour is analysed based on the Cohen-Turnbull theory of molecular diffusion in a liquid.On trouve que la viscosité du latex monodispersé de polystyrène croit anormalement au voisinage du point de transition ordre-désordre lorsqu'on approche dans la phase desordonnee. On analyse le comportement anormal en utilisaut la théorie de Cohen-Turnbull pour la diffusion moléculaire du liquide
In vitro activities of furoquinoline and acridone alkaloids against Plasmodium falciparum
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