An innovative replica exchange (parallel tempering) method called replica exchange with solute tempering (REST) for the efficient sampling of aqueous protein solutions is presented here. The method bypasses the poor scaling with system size of standard replica exchange and thus reduces the number of replicas (parallel processes) that must be used. This reduction is accomplished by deforming the Hamiltonian function for each replica in such a way that the acceptance probability for the exchange of replica configurations does not depend on the number of explicit water molecules in the system. For proof of concept, REST is compared with standard replica exchange for an alanine dipeptide molecule in water. The comparisons confirm that REST greatly reduces the number of CPUs required by regular replica exchange and increases the sampling efficiency. This method reduces the CPU time required for calculating thermodynamic averages and for the ab initio folding of proteins in explicit water. molecular dynamics ͉ Monte Carlo ͉ parallel tempering ͉ protein solutions ͉ rough energy landscapes S ampling the conformation space of complex systems, such as proteins, is a notoriously difficult problem in structural biology and theoretical chemistry. The difficulty arises from the infrequent crossings of high-energy barriers between local energy minima, leading to local trapping for long times and concomitant quasi-ergodicity in the sampling. Many methods have been devised to overcome the problem of quasi-ergodicity. These methods include the multicanonical ensemble method (1-3), the simulated tempering method (4-6), and the parallel tempering or replica exchange method (REM) (7-9).The first two methods require a non-Boltzmann weight factor arrived at by iteration. For systems with rough energy landscapes, such as proteins dissolved in explicit water, obtaining the weight factor is not a trivial process. Thus, the REM has been attracting more and more attention because the standard Boltzmann weight factor can be used. By using high-temperature replicas to overcome the energy barrier, the REM has proven to be a useful method for sampling phase space (10, 11).For the standard REM, the number of replicas needed increases as O(f 1/2 ), where f is the solution's total number of degrees of freedom (12). Even for a relatively small biomolecular system consisting of one ␤-hairpin protein molecule dissolved in water (4,342 atoms in all), 64 replicas were needed to cover the temperature range between 270 and 695 K with a nonvanishing acceptance ratio for replica exchange (13). This requirement severely restricts the applicability of REM to reasonably small systems, unless one has access to a massively parallel computer.The main reason that a large number of replicas are required is that the overall Hamiltonian grows with system size. The acceptance probability for the exchange of configurations between two replicas at different temperatures is exp(⌬␤⌬E), a quantity that depends exponentially on the change in energy. For a larger system, o...

How organ size is controlled in mammals is not currently understood. In Drosophila the Hippo signaling pathway functions to suppress growth in imaginal discs and has been suggested to control organ size. To investigate the role of hippo signaling in regulation of mammalian organ size we have generated conditional alleles of Sav1 , mst1 , and mst2 , orthologs of Drosophila Salvador and hippo , respectively. Specific deletion of both mst1 and mst2 in hepatocytes results in significantly enlarged livers due to excessive proliferation. By the age of 5–6 months, mst1/2 conditional mutant livers have multiple foci of liver tumors, indicating that the combined activities of mst1 and mst2 act as redundant tumor suppressors in hepatocytes. Similar findings were obtained with liver-specific deletion of Sav1 , a second core Hippo signaling component that facilitates activation of mst1 and mst2 . Tumors from sav1 mutants exhibited varied morphology, suggesting a mixed-lineage origin of tumor-initiating cells. Transcriptional profiling of liver tissues from both mst1/2 and sav1 conditional mutants revealed a network of Hippo signaling regulated genes with specific enrichment for genes involved in immune and inflammatory responses. Histological and immunological characterization of mst1/2 double mutant liver tissues revealed abundant accumulation of adult facultative stem cells termed oval cells in periductal regions. Because oval cells induction is commonly associated with liver injury and tumor formation, it is likely that these cells contribute to the enlarged livers and hepatomas that we observe in sav1 and mst1/2 mutants. Taken together, our results demonstrate that the Hippo signaling pathway is a critical regulator of mammalian liver growth and a potent suppressor of liver tumor formation.

The multiscale coarse-graining ͑MS-CG͒ method ͓S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 ͑2005͒; J. Chem. Phys. 123, 134105 ͑2005͔͒ employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force ͑PMF͒ governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM + / NO 3 − ionic liquid are provided to illustrate the method.

We propose a general methodology for calculating the self-diffusion tensor from molecular dynamics for a liquid with a liquid-gas or liquid-solid interface. The standard method used in bulk fluids, based on computing the mean square displacement as a function of time and extracting the asymptotic linear time dependence from this, is not valid for systems with interfaces or for confined fluids. The method proposed here is based on imposing virtual boundary conditions on the molecular system and computing survival probabilities and specified time correlation functions in different layers of the fluid up to and including the interfacial layer. By running dual simulations, one based on MD and the other based on Langevin dynamics, using the same boundary conditions, one can fit the Langevin survival probability at long times to the MD computed survival probability, thereby determining the diffusion coefficient as a function of distance of the layers from the interface. We compute the elements of the diffusion tensor of water as a function of distance from the liquid vapor interface of water. Far from the interface the diffusion tensor is found to be isotropic, as 2

Marked hydration changes occur during the self-assembly of the melittin protein tetramer in water. Hydrophobicity induces a drying transition in the gap between simple sufficiently large (more than 1 nm(2)) strongly hydrophobic surfaces as they approach each other, resulting in the subsequent collapse of the system, as well as a depletion of water next to single surfaces. Here we investigate whether the hydrophobic induced collapse of multidomain proteins or the formation of protein oligimers exhibits a similar drying transition. We performed computer simulations to study the collapse of the tetramer of melittin in water, and observed a marked water drying transition inside a nanoscale channel of the tetramer (with a channel size of up to two or three water-molecule diameters). This transition, although occurring on a microscopic length scale, is analogous to a first-order phase transition from liquid to vapour. We find that this drying is very sensitive to single mutations of the three isoleucines to less hydrophobic residues and that such mutations in the right locations can switch the channel from being dry to being wet. Thus, quite subtle changes in hydrophobic surface topology can profoundly influence the drying transition. We show that, even in the presence of the polar protein backbone, sufficiently hydrophobic protein surfaces can induce a liquid-vapour transition providing an enormous driving force towards further collapse. This behaviour was unexpected because of the absence of drying in the collapse of the multidomain protein 2,3-dihydroxybiphenyl dioxygenase (BphC).

The pericentric inversion of chromosome 16 [inv(16)(p13q22)] is a characteristic karyotypic abnormality associated with acute myeloid leukemia, most commonly of the M4Eo subtype. The 16p and 16q breakpoints were pinpointed by yeast artificial chromosome and cosmid cloning, and the two genes involved in this inversion were identified. On 16q the inversion occurred near the end of the coding region for CBF beta, also known as PEBP2 beta, a subunit of a heterodimeric transcription factor regulating genes expressed in T cells; on 16p a smooth muscle myosin heavy chain (SMMHC) gene (MYH11) was interrupted. In six of six inv(16) patient samples tested, an in-frame fusion messenger RNA was demonstrated that connected the first 165 amino acids of CBF beta with the tail region of SMMHC. The repeated coiled coil of SMMHC may result in dimerization of the CBF beta fusion protein, which in turn would lead to alterations in transcriptional regulation and contribute to leukemic transformation.

Irradiation-attenuated sporozoite vaccinations confer sterile protection against malaria infection in animal models and humans. Persistent, nonreplicating parasite forms in the liver are presumably necessary for the maintenance of sterile immunity. A novel vaccine approach uses genetically attenuated parasites (GAPs) that undergo arrested development during liver infection. The fate of GAPs after immunization, their persistence in vaccinated animals, and the immune mechanisms that mediate protection are unknown. To examine the developmental defects of genetically attenuated liver stages in vivo, we created deletions of the UIS3 and UIS4 loci in the Plasmodium yoelii rodent malaria model (Pyuis3[-] and Pyuis4[-]). The low 50% infectious dose of P. yoelii in BALB/c mice provides the most sensitive infectivity model. We show that P. yoelii GAPs reach the liver, invade hepatocytes, and develop a parasitophorous vacuole but do not significantly persist 40 h after infection. A single dose of Pyuis4(-) sporozoites conferred complete protection, but full protection by Pyuis3(-) sporozoites required at least 2 immunizations. CD8(+) T cells were essential for protection, but CD4(+) T cells were not. Our results show that genetically distinct GAPs confer different degrees of protective efficacy and that live vaccine persistence in the liver is not necessary to sustain long-lasting protection. These findings have important implications for the development of a P. falciparum GAP malaria vaccine.

An effective force coarse-graining (EF-CG) method is presented in this paper that complements the more general multiscale coarse-graining (MS-CG) methodology. The EF-CG method determines effective pairwise forces between coarse-grained sites by averaging over the atomistic forces between the corresponding atomic groups in configurations sampled from equilibrium all-atom molecular dynamics simulations. The EF-CG method extracts the transferable part of the MS-CG force field at the cost of reduced accuracy in reproducing certain structural properties. Therefore, the EF-CG method provides an alternative to the MS-CG approach for determining CG force fields that give improved transferability but reduced structural accuracy. The EF-CG method is especially suitable for coarse-graining large molecules with high symmetry, such as bulky organic molecules, and for studying complex phenomena across a range of thermodynamic conditions. The connection between the EF-CG and MS-CG approaches as well as the limitations of the EF-CG method are also discussed. Numerical results for neopentane, methanol and ionic liquid systems illustrate the utility of the method.