522 research outputs found
Fluctuation-Induced Interactions between Rods on Membranes and Interfaces
We consider the interaction between two rods embedded in a fluctuating
surface which is governed by either surface tension or rigidity. The
modification of fluctuations by the rods leads to an attractive long-range
interaction that falls off as with their separation. The orientational
dependence of the resulting interaction is non-trivial and may lead to
interesting patterns of rod-like objects on such surfaces.Comment: Revtex, 10 pages, one figur
Collective shuttling of attracting particles in asymmetric narrow channels
The rectification of a single file of attracting particles subjected to a low
frequency ac drive is proposed as a working mechanism for particle shuttling in
an asymmetric narrow channel. Increasing the particle attraction results in the
file condensing, as signalled by the dramatic enhancement of the net particle
current. Magnitude and direction of the current become extremely sensitive to
the actual size of the condensate, which can then be made to shuttle between
two docking stations, transporting particles in one direction, with an
efficiency much larger than conventional diffusive models predict
Ligand binding and conformational dynamics of the E. coli nicotinamide nucleotide transhydrogenase revealed by hydrogen/deuterium exchange mass spectrometry
Nicotinamide nucleotide transhydrogenases are integral membrane proteins that utilizes the proton motive force to reduce NADP+ to NADPH while converting NADH to NAD+. Atomic structures of various transhydrogenases in different ligand-bound states have become available, and it is clear that the molecular mechanism involves major conformational changes. Here we utilized hydrogen/deuterium exchange mass spectrometry (HDX-MS) to map ligand binding sites and analyzed the structural dynamics of E. coli transhydrogenase. We found different allosteric effects on the protein depending on the bound ligand (NAD+, NADH, NADP+, NADPH). The binding of either NADP+ or NADPH to domain III had pronounced effects on the transmembrane helices comprising the proton-conducting channel in domain II. We also made use of cyclic ion mobility separation mass spectrometry (cyclic IMS-MS) to maximize coverage and sensitivity in the transmembrane domain, showing for the first time that this technique can be used for HDX-MS studies. Using cyclic IMS-MS, we increased sequence coverage from 68 % to 73 % in the transmembrane segments. Taken together, our results provide important new insights into the transhydrogenase reaction cycle and demonstrate the benefit of this new technique for HDX-MS to study ligand binding and conformational dynamics in membrane proteins
Phase Behaviour of Amphiphilic Monolayers: Theory and Simulation
Coarse grained models of monolayers of amphiphiles (Langmuir monolayers) have
been studied theoretically and by computer simulations. We discuss some of the
insights obtained with this approach, and present new simulation results which
show that idealised models can successfully reproduce essential aspects of the
generic phase behaviour of Langmuir monolayers.Comment: To appear in J. Phys.: Cond. Matte
Proton Wires in an Electric Field: the Impact of Grotthuss Mechanism on Charge Translocation
We present the results of the modeling of proton translocation in finite
H-bonded chains in the framework of two-stage proton transport model. We
explore the influence of reorientation motion of protons, as well as the effect
of electric field and proton correlations on system dynamics. An increase of
the reorientation energy results in the transition of proton charge from the
surrounding to the inner water molecules in the chain. Proton migration along
the chain in an external electric field has a step-like character, proceeding
with the occurrence of electric field threshold-type effects and drastic
redistribution of proton charge. Electric field applied to correlated chains
induces first a formation of ordered dipole structures for lower field
strength, and than, with a further field strength increase, a stabilization of
states with Bjerrum D-defects. We analyze the main factors responsible for the
formation/annihilation of Bjerrum defects showing the strong influence of the
complex interplay between reorientation energy, electric field and temperature
in the dynamics of proton wire.Comment: 28 pages, 9 figure
Fluctuation-Induced Interactions between Rods on a Membrane
We consider the interaction between two rods embedded in a fluctuating
surface. The modification of fluctuations by the rods leads to an attractive
long-range interaction between them. We consider fluctuations governed by
either surface tension (films) or bending rigidity (membranes). In both cases
the interaction falls off with the separation of the rods as . The
orientational part of the interaction is proportional to in the former case, and to in the latter, where and
are angles between the rods and the line joining them. These
interactions are somewhat reminiscent of dipolar forces and will tend to align
collections of such rods into chains.Comment: REVTEX, 14 pages, with 2 Postscript figure
Structure of symmetric and asymmetric "ripple" phases in lipid bilayers
We reproduce the symmetric and asymmetric ``rippled'' states of
lipid membranes by Monte Carlo simulations of a coarse-grained molecular model
for lipid-solvent mixtures. The structure and properties compare favorably with
experiments. The asymmetric ripple state is characterized by a periodic array
of fully interdigitated ``defect'' lines. The symmetric ripple state maintains
a bilayer structure, but is otherwise structurally similar. The formation of
both ripple states is driven by the propensity of lipid molecules with large
head groups to exhibit splay.Comment: 4 pages, 4 figure
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
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
An updated genome-scale reconstruction of the metabolic network in Escherichia coli K-12 MG1655 is presented. This updated metabolic reconstruction includes: (1) an alignment with the latest genome annotation and the metabolic content of EcoCyc leading to the inclusion of the activities of 1260 ORFs, (2) characterization and quantification of the biomass components and maintenance requirements associated with growth of E. coli and (3) thermodynamic information for the included chemical reactions. The conversion of this metabolic network reconstruction into an in silico model is detailed. A new step in the metabolic reconstruction process, termed thermodynamic consistency analysis, is introduced, in which reactions were checked for consistency with thermodynamic reversibility estimates. Applications demonstrating the capabilities of the genome-scale metabolic model to predict high-throughput experimental growth and gene deletion phenotypic screens are presented. The increased scope and computational capability using this new reconstruction is expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism
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