Activation pathway of Src kinase reveals intermediate states as targets for drug design.

Unregulated activation of Src kinases leads to aberrant signalling, uncontrolled growth and differentiation of cancerous cells. Reaching a complete mechanistic understanding of large-scale conformational transformations underlying the activation of kinases could greatly help in the development of therapeutic drugs for the treatment of these pathologies. In principle, the nature of conformational transition could be modelled in silico via atomistic molecular dynamics simulations, although this is very challenging because of the long activation timescales.

Synthesis and reactivity of two-coordinate Ni(I) alkyl and aryl complexes.

Reaction of [(IPr)Ni(μ-Cl)]2 (1-Cl; IPr = 1,3-bis(2,6-diisopropylphenyl)imidazolin-2-ylidene) with ClMg{CH(SiMe3)2}·Et2O affords (IPr)Ni{CH(SiMe3)2} (2), a two-coordinate Ni(I) alkyl complex. An analogous two-coordinate aryl derivative, (IPr)Ni(dmp) (dmp = 2,6-dimesitylphenyl), can be similarly prepared from Li(dmp) and 1-Cl. Reaction of 2 with alkyl bromides gives the three-coordinate Ni(II) alkyl halide complex (IPr)Ni{CH(SiMe3)2}Br.

A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations.

OmpF, a multiionic porin from Escherichia coli, is a useful protypical model system for addressing general questions about electrostatic interactions in the confinement of an aqueous molecular pore. Here, favorable anion locations in the OmpF pore were mapped by anomalous X-ray scattering of Br(–) ions from four different crystal structures and compared with Mg(2+) sites and Rb(+) sites from a previous anomalous diffraction study to provide a complete picture of cation and anion transfer paths along the OmpF channel. By comparing structures with various crystallization conditions, we find that anions bind in discrete clusters along the entire length of the OmpF pore, whereas cations find conserved binding sites with the extracellular, surface-exposed loops.

Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations.

A computational method is developed to allow molecular dynamics simulations of biomembrane systems under realistic ionic gradients and asymmetric salt concentrations while maintaining the conventional periodic boundary conditions required to minimize finite-size effects in an all-atom explicit solvent representation. The method, which consists of introducing a nonperiodic energy step acting on the ionic species at the edge of the simulation cell, is first tested with illustrative applications to a simple membrane slab model and a phospholipid membrane bilayer. The nonperiodic energy-step method is then used to calculate the reversal potential of the bacterial porin OmpF, a large cation-specific β-barrel channel, by simulating the I-V curve under an asymmetric 10:1 KCl concentration gradient.

Computational analysis of the binding specificity of Gleevec to Abl, c-Kit, Lck, and c-Src tyrosine kinases.

Gleevec, a well-known cancer therapeutic agent, is an effective inhibitor of several tyrosine kinases, including Abl and c-Kit, but displays less potency to inhibit closely homologous tyrosine kinases, such as Lck and c-Src. Because many structural features of the binding site are highly conserved in these homologous kinases, the molecular determinants responsible for the binding specificity of Gleevec remain poorly understood. To address this issue, free energy perturbation molecular dynamics (FEP/MD) simulations with explicit solvent was used to compute the binding affinity of Gleevec to Abl, c-Kit, Lck, and c-Src.

A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids.

A polarizable force field of saturated phosphatidylcholine-containing lipids based on the classical Drude oscillator model is optimized and used in molecular dynamics simulations of bilayer and monolayer membranes. The hierarchical parametrization strategy involves the optimization of parameters for small molecules representative of lipid functional groups, followed by their application in larger model compounds and full lipids. The polar headgroup is based on molecular ions tetramethyl ammonium and dimethyl phosphate, the esterified glycerol backbone is based on methyl acetate, and the aliphatic lipid hydrocarbon tails are based on linear alkanes.

Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field.

The accuracy of empirical force fields is critical for meaningful molecular dynamics simulations of concentrated ionic solutions. Current models are typically developed on the basis of single ion properties such as the monohydrate energy in the gas phase, or the absolute hydration free energy at infinite dilution. However, the failure of these models to represent accurately the properties of concentrated solutions cannot be excluded.

The vanadyl chelate bis(acetylacetonato)oxovanadium(IV) increases the fractional uptake of 2-(fluorine-18)-2-deoxy-D-glucose by cultured human breast carcinoma cells.

Detection of breast cancer by positron emission tomography (PET) imaging with 2-(fluorine-18)-2-deoxy-D-glucose (FDG) as the tracer molecule is limited in part by both tumor dimension and metabolic activity. While some types of aggressive breast cancers are associated with a high capacity for FDG uptake, more indolent breast cancers are characterized by low FDG uptake. Moreover, detection of malignant lesions in most clinical settings requires tumor dimensions ≥10 mm.

Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron-electron resonance spectroscopy.

DEER (double electron-electron resonance) spectroscopy is a powerful pulsed ESR (electron spin resonance) technique allowing the determination of spin-spin distance histograms between site-directed nitroxide label sites on a protein in their native environment. However, incorporating ESR/DEER data in structural refinement is challenging because the information from the large number of distance histograms is complex and highly coupled. Here, a novel restrained-ensemble molecular dynamics simulation method is developed to incorporate the information from multiple ESR/DEER distance histograms simultaneously.

On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method.

An issue of general interest in computer simulations is to incorporate information from experiments into a structural model. An important caveat in pursuing this goal is to avoid corrupting the resulting model with spurious and arbitrary biases. While the problem of biasing thermodynamic ensembles can be formulated rigorously using the maximum entropy method introduced by Jaynes, the approach can be cumbersome in practical applications with the need to determine multiple unknown coefficients iteratively.

Explaining why Gleevec is a specific and potent inhibitor of Abl kinase.

Tyrosine kinases present attractive drug targets for specific types of cancers. Gleevec, a well-known therapeutic agent against chronic myelogenous leukemia, is an effective inhibitor of Abl tyrosine kinase. However, Gleevec fails to inhibit closely homologous tyrosine kinases, such as c-Src.

The binding of antibiotics in OmpF porin.

The structure of OmpF porin in complex with three common antibiotics (zwitterionic ampicillin, anionic ertapenem, and di-anionic carbenicillin) was determined using X-ray crystallography. The three antibiotics are found to bind within the extracellular and periplasmic pore vestibules, away from the narrow OmpF constriction zone. Using the X-ray structures as a starting point, nonequilibrium molecular dynamics simulations with an applied membrane voltage show that ionic current through the OmpF channel is blocked with bound ampicillin, but not with bound carbenicillin.

Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer.

An extremely scalable computational strategy is described for calculations of the potential of mean force (PMF) in multidimensions on massively distributed supercomputers. The approach involves coupling thousands of umbrella sampling (US) simulation windows distributed to cover the space of order parameters with a Hamiltonian molecular dynamics replica-exchange (H-REMD) algorithm to enhance the sampling of each simulation. In the present application, US/H-REMD is carried out in a two-dimensional (2D) space and exchanges are attempted alternatively along the two axes corresponding to the two order parameters.

Rethinking the (im)possible in evolution.

This paper will discuss the philosophical background to evolutionary theory and present multiple counterfactuals to each of the following seven empirically unsustainable but nonetheless widespread assumptions about genomic (DNA-based) evolution: 1. "All heredity transmission occurs from parent to progeny" 2. "Mutations are the result of inevitable replication errors" 3.

Ion binding sites and their representations by reduced models.

The binding of small metal ions to complex macromolecular structures is typically dominated by strong local interactions of the ion with its nearest ligands. Progress in understanding the molecular determinants of ion selectivity can often be achieved by considering simplified reduced models comprised of only the most important ion-coordinating ligands. Although the main ingredients underlying simplified reduced models are intuitively clear, a formal statistical mechanical treatment is nonetheless necessary in order to draw meaningful conclusions about complex macromolecular systems.

RKIP Suppresses Breast Cancer Metastasis to the Bone by Regulating Stroma-Associated Genes.

In the past decade cancer research has recognized the importance of tumorstroma interactions for the progression of primary tumors to an aggressive and invasive phenotype and for colonization of new organs in the context of metastasis. The dialogue between tumor cells and the surrounding stroma is a complex and dynamic phenomenon, as many cell types and soluble factors are involved. While the function of many of the players involved in this cross talk have been studied, the regulatory mechanisms and signaling pathways that control their expression haven't been investigated in depth.

Crystal structure of an RNA polymerase ribozyme in complex with an antibody fragment.

All models of the RNA world era invoke the presence of ribozymes that can catalyse RNA polymerization. The class I ligase ribozyme selected in vitro 15 years ago from a pool of random RNA sequences catalyses formation of a 3',5'-phosphodiester linkage analogous to a single step of RNA polymerization. Recently, the three-dimensional structure of the ligase was solved in complex with U1A RNA-binding protein and independently in complex with an antibody fragment.

Ouabain binding site in a functioning Na+/K+ ATPase.

The Na(+)/K(+) ATPase is an almost ubiquitous integral membrane protein within the animal kingdom. It is also the selective target for cardiotonic derivatives, widely prescribed inhibitors for patients with heart failure. Functional studies revealed that ouabain-sensitive residues distributed widely throughout the primary sequence of the protein.

Synthesis and characterization of three-coordinate Ni(III)-imide complexes.

A new family of low-coordinate nickel imides supported by 1,2-bis(di-tert-butylphosphino)ethane was synthesized. Oxidation of nickel(II) complexes led to the formation of both aryl- and alkyl-substituted nickel(III)-imides, and examples of both types have been isolated and fully characterized. The aryl substituent that proved most useful in stabilizing the Ni(III)-imide moiety was the bulky 2,6-dimesitylphenyl.

A conserved archaeal pathway for tail-anchored membrane protein insertion.

Eukaryotic tail-anchored (TA) membrane proteins are inserted into the endoplasmic reticulum by a post-translational TRC40 pathway, but no comparable pathway is known in other domains of life. The crystal structure of an archaebacterial TRC40 sequence homolog bound to ADP•AlF(4) (-) reveals characteristic features of eukaryotic TRC40, including a zinc-mediated dimer and a large hydrophobic groove. Moreover, archaeal TRC40 interacts with the transmembrane domain of TA substrates and directs their membrane insertion.

Shear thickening of F-actin networks crosslinked with non-muscle myosin IIB.

The material properties of cytoskeletal F-actin networks facilitate a broad range of cellular behaviors, whereby in some situations cell shape is preserved in the presence of force and, at other times, force results in irreversible shape change. These behaviors strongly suggest that F-actin networks can variably deform elastically or viscously. While a significant amount is known about the regulation of the elastic stiffness of F-actin networks, our understanding of the regulation of viscous behaviors of F-actin networks is largely lacking.

A two-coordinate nickel imido complex that effects C−H amination.

An exceptionally low coordinate nickel imido complex, (IPr*)Ni═N(dmp) (2) (dmp = 2,6-dimesitylphenyl), has been prepared by the elimination of N2 from a bulky aryl azide in its reaction with (IPr*)Ni(η6-C7H8) (1). The solid-state structure of 2 features two-coordinate nickel with a linear C−Ni−N core and a short Ni−N distance, both indicative of multiple-bond character. Computational studies using density functional theory showed a Ni═N bond dominated by Ni(dπ)−N(pπ) interactions, resulting in two nearly degenerate singly occupied molecular orbitals (SOMOs) that are Ni−N π* in character.

Hydrogen-atom abstraction from Ni(I) phosphido and amido complexes gives phosphinidene and imide ligands.

Hydrogen-atom abstraction from M-E(H) to generate M═E-containing complexes (E = PR, NR) is not well studied because only a few complexes are known to undergo such reactions. Hydrogen-atom abstraction from nickel(I) phosphide and amide complexes led to the corresponding phosphinidene and imide compounds. These reactions are unparalleled in the organometallic chemistry of nickel and feature an unusual example of a transition-metal phosphinidene synthesized by hydrogen-atom abstraction.