How proteins open fusion pores: insights from molecular simulations

Fusion proteins can play a versatile and involved role during all stages of the fusion reaction. Their roles go far beyond forcing the opposing membranes into close proximity to drive stalk formation and fusion. Molecular simulations have played a central role in providing a molecular understanding of how fusion proteins actively overcome the free energy barriers of the fusion reaction up to the expansion of the fusion pore. Unexpectedly, molecular simulations have revealed a preference of the biological fusion reaction to proceed through asymmetric pathways resulting in the formation of, e.g., a stalk-hole complex, rim-pore, or vertex pore. Force-field based molecular simulations are now able to directly resolve the minimum free-energy path in protein-mediated fusion as well as quantifying the free energies of formed reaction intermediates. Ongoing developments in Graphics Processing Units (GPUs), free energy calculations, and coarse-grained force-fields will soon gain additional insights into the diverse roles of fusion proteins

Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations

The molecular packing details of lipids in planar bilayers are well characterized. For curved bilayers, however, little data is available. In this paper we study the effect of temperature and membrane composition on the structural and dynamical properties of a liposomal membrane in the limit of high curvature (liposomal diameter of 15-20 nm), using coarse grained molecular dynamics simulations. Both pure dipalmitoyl phosphatidylcholine (DPPC) liposomes and binary mixtures of DPPC and either dipalmitoyl phosphatidylethanolamine (DPPE) or polyunsaturated dilinoleylphosphatidylcholine (DLiPC) lipids are modeled. We take special care in the equilibration of the liposomes requiring lipid flip-flopping, which can be facilitated by the temporary insertion of artificial pores. The equilibrated liposomes show some remarkable properties. Curvature induces membrane thinning and reduces the thermal expansivity of the membrane. In the inner monolayer the lipid head groups are very closely packed and dehydrated, and the lipids tails relatively disordered. The opposite packing effects are seen in the outer monolayer. In addition, we noticed an increased tendency of the lipid tails to backfold toward the interface in the outer monolayer. The distribution of lipids over the monolayers was found to be strongly temperature dependent. Higher temperatures favor more equally populated monolayers. Relaxation times of the lipid tails were found to increase with increasing curvature, with the lipid tails in the outer monolayer showing a significant slower dynamics compared to the lipid tails in the inner monolayer. In the binary systems there is a clear tendency toward partial transversal demixing of the two components, with especially DPPE enriched in the inner monolayer. This observation is in line with a static shape concept which dictates that inverted-cone shaped lipids such as DPPE and DLiPC would prefer the concave volume of the inner monolayer. However, our results for DLiPC show that another effect comes into play that is almost equally strong and provides a counter-acting driving force toward the outer, rather than the inner monolayer. This effect is the ability of the polyunsaturated tails of DLiPC to backfold, which is advantageous in the outer monolayer. We speculate that polyunsaturated lipids in biological membranes may play an important role in stabilizing both positive and negative regions of curvature.</p

On The Implementation Of Experimental Solenoids In MAD-X And Their Effect On Coupling In The LHC

The betatron coupling introduced by the experimental solenoids in the LHC is small at injection and negligible at collision energy. We present a study of these effects and look at possible corrections. Additionally we report about the implementation of solenoids in the MAD-X program. A thin solenoid version is also made available for tracking purposes

Final-Focus Schemes for CLIC at 3 TeV

We discuss benefits and drawbacks of two different final-focus schemes for CLIC at 3 TeV centre-of-mass (c.m.) energy, by examining tolerances, tunability and potential background for a 3.3-km long baseline final-focus system and a shorter advanced design

Damping rings for CLIC

The Compact Linear Colider (CLIC) is designed to operate at 3 TeV centre-of-mass energy with a total luminosity of 10^35 cm^-2 s^-1. The overall system design leads to extremely demanding requirements on the bunch trains injected into the main libac at frequency of 100 Hz. In particular, the emittances of the intense bunches have to be about an order of magnitude smaller than presently achieved. We describe our approach to finding a damping ring design capable of meeting these requirements. Besides lattice design, emittance and damping rate considerations, a number of scattering and instability effects have to be incorporated into the optimisation of parameters. Among these, intra-bem scattering and the electron cloud effect are two of the most significant

Optics Flexibility and Dispersion Matching at Injection into the LHC

The LHC requires very precise matching of transfer line and LHC optics to minimise emittance blow-up and tail repopulation at injection. The recent addition of a comprehensive transfer line collimation system to improve the protection against beam loss has created additional matching constraints and consumed a significant part of the flexibility contained in the initial optics design of the transfer lines. Optical errors, different injection configurations and possible future optics changes require however to preserve a certain tuning range. Here we present methods of tuning optics parameters at the injection point by using orbit correctors in the main ring, with the emphasis on dispersion matching. The benefit of alternative measures to enhance the flexibility is briefly discussed

A more robust and flexible lattice for LHC

To correct more efficiently the arc dispersion, the exact antisymmetry of the LHC optics is now broken, except in the low-b triplets common to the two rings. A new quadrupole is added between the experimental insertions and the dispersion suppressors and several arc quadrupoles are complemented by a small trim quadrupole. The larger number of parameters gives flexibility to the lattice and allows a partial separation of the optical functions, with a decrease of the total number of quadrupole units. It is possible to change rather freely the phase advances of the arc cells. The nominal tunes are split by 4 units to reduce coupling. The bin boot tuning range in the experimental low-b is significantly increased, allowing e.g. a larger beam separation at injection. The super-periodicity of LHC remains 1. We plan to study whether it can be increased within the LHC hardware constraint

PspF-binding domain PspA1-144 and the PspA·F complex: New insights into the coiled-coil-dependent regulation of AAA+ proteins.

Phage shock protein A (PspA) belongs to the highy conserved PspA/IM30 family and is a key component of the stress inducible Psp system in Escherichia coli. One of its central roles is the regulatory interaction with the transcriptional activator of this system, the σ54 enhancer binding protein PspF, a member of the AAA+ protein family. The PspA/F regulatory system has been intensively studied and serves as a paradigm for AAA+ enzyme regulation by trans-acting factors. However, the molecular mechanism of how exactly PspA controls the activity of PspF and hence σ54-dependent expression of the psp genes is still unclear. To approach this question, we identified the minimal PspF-interacting domain of PspA, solved its structure, determined its affinity to PspF and the dissociation kinetics, identified residues that are potentially important for PspF regulation and analyzed effects of their mutation on PspF in vivo and in vitro. Our data indicate that several characteristics of AAA+ regulation in the PspA·F complex resemble those of the AAA+ unfoldase ClpB, with both proteins being regulated by a structurally highly conserved coiled-coil domain. The convergent evolution of both regulatory domains points to a general mechanism to control AAA+ activity for divergent physiological tasks via coiled-coil domains