Pu Liu

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.

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.

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.

We propose a general methodology for calculating the self-diffusion tensor from molecular dynamics (MD) 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 time 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 expected, and the diffusion coefficient has the value D ≈ 0.22 Å2/ps, in agreement with what is found in the bulk liquid. In the interfacial region the diffusion tensor is axially anisotropic, with values of D∥ ≈ 0.8 Å2/ps and D⊥ ≈ 0.5 Å2/ps for the components parallel and normal the interface surface, respectively. We also show that diffusion in confined geometries can be calculated by imposing appropriate boundary conditions on the molecular system and computing time correlation functions of the eigenfunctions of the diffusion operator corresponding to the same boundary conditions.