Systematic drug perturbations on cancer cells reveal diverse exit paths from proliferative state.

During a cell state transition, cells travel along trajectories in a gene expression state space. This dynamical systems framework complements the traditional concept of molecular pathways that drive cell phenotype switching. To expose the structure that hinders cancer cells from exiting robust proliferative state, we assessed the perturbation capacity of a drug library and identified 16 non-cytotoxic compounds that stimulate MCF7 breast cancer cells to exit from proliferative state to differentiated state.

Fullerene-based inhibitors of HIV-1 protease.

A series of Fmoc-Phe(4-aza-C60)-OH of fullerene amino acid derived peptides have been prepared by solid phase peptide synthesis, in which the terminal amino acid, Phe(4-aza-C60)-OH, is derived from the dipolar addition to C60 of the Fmoc-Nα-protected azido amino acids derived from phenylalanine: Fmoc-Phe(4-aza-C60)-Lys3-OH (1), Fmoc-Phe(4-aza-C60)-Pro-Hyp-Lys-OH (2), and Fmoc-Phe(4-aza-C60)-Hyp-Hyp-Lys-OH (3). The inhibition constant of our fullerene aspartic protease PRIs utilized FRET-based assay to evaluate the enzyme kinetics of HIV-1 PR at various concentrations of inhibitors. Simulation of the docking of the peptide Fmoc-Phe-Pro-Hyp-Lys-OH overestimated the inhibition, while the amino acid PRIs were well estimated.

High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach.

Interactions between membrane proteins are of great biological significance and are consequently an important target for pharmacological intervention. Unfortunately, it is still difficult to obtain detailed views on such interactions, both experimentally, where the environment hampers atomic resolution investigation, and computationally, where the time and length scales are problematic. Coarse grain simulations have alleviated the later issue, but the slow movement through the bilayer, coupled to the long life times of nonoptimal dimers, still stands in the way of characterizing binding distributions.

Non-genetic cancer cell plasticity and therapy-induced stemness in tumour relapse: 'What does not kill me strengthens me'.

Therapy resistance and tumour relapse after drug therapy are commonly explained by Darwinian selection of pre-existing drug-resistant, often stem-like cancer cells resulting from random mutations. However, the ubiquitous non-genetic heterogeneity and plasticity of tumour cell phenotype raises the question: are mutations really necessary and sufficient to promote cell phenotype changes during tumour progression? Cancer therapy inevitably spares some cancer cells, even in the absence of resistant mutants. Accumulating observations suggest that the non-killed, residual tumour cells actively acquire a new phenotype simply by exploiting their developmental potential.

Nonequilibrium population dynamics of phenotype conversion of cancer cells.

Tumorigenesis is a dynamic biological process that involves distinct cancer cell subpopulations proliferating at different rates and interconverting between them. In this paper we proposed a mathematical framework of population dynamics that considers both distinctive growth rates and intercellular transitions between cancer cell populations. Our mathematical framework showed that both growth and transition influence the ratio of cancer cell subpopulations but the latter is more significant.

Designing of multi-targeted molecules using combination of molecular screening and in silico drug cardiotoxicity prediction approaches.

We have previously investigated and reported a set of phenol- and indole-based derivatives at the binding pockets of carbonic anhydrase isoenzymes using in silico and in vitro analyses. In this study, we extended our analysis to explore multi-targeted molecules from this set of compounds. Thus, 26 ligands are screened at the binding sites of 229 proteins from 5 main enzyme family classes using molecular docking algorithms.

Thiol redox biochemistry: insights from computer simulations.

Thiol redox chemical reactions play a key role in a variety of physiological processes, mainly due to the presence of low-molecular-weight thiols and cysteine residues in proteins involved in catalysis and regulation. Specifically, the subtle sensitivity of thiol reactivity to the environment makes the use of simulation techniques extremely valuable for obtaining microscopic insights. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of selected relevant issues in thiol redox biochemistry, such as investigations on (1) the protonation state of cysteine in protein, (2) two-electron oxidation of thiols by hydroperoxides, chloramines, and hypochlorous acid, (3) mechanistic and kinetics aspects of the de novo formation of disulfide bonds and thiol-disulfide exchange, (4) formation of sulfenamides, (5) formation of nitrosothiols and transnitrosation reactions, and (6) one-electron oxidation pathways.

The ryanodine receptor store-sensing gate controls Ca2+ waves and Ca2+-triggered arrhythmias.

Spontaneous Ca(2+) release from intracellular stores is important for various physiological and pathological processes. In cardiac muscle cells, spontaneous store overload-induced Ca(2+) release (SOICR) can result in Ca(2+) waves, a major cause of ventricular tachyarrhythmias (VTs) and sudden death. The molecular mechanism underlying SOICR has been a mystery for decades.

Sodium channel selectivity and conduction: prokaryotes have devised their own molecular strategy.

Striking structural differences between voltage-gated sodium (Nav) channels from prokaryotes (homotetramers) and eukaryotes (asymmetric, four-domain proteins) suggest the likelihood of different molecular mechanisms for common functions. For these two channel families, our data show similar selectivity sequences among alkali cations (relative permeability, Pion/PNa) and asymmetric, bi-ionic reversal potentials when the Na/K gradient is reversed. We performed coordinated experimental and computational studies, respectively, on the prokaryotic Nav channels NaChBac and NavAb.

Systematic genetic analysis of transcription factors to map the fission yeast transcription-regulatory network.

Mapping transcriptional-regulatory networks requires the identification of target genes, binding specificities and signalling pathways of transcription factors. However, the characterization of each transcription factor sufficiently for deciphering such networks remains laborious. The recent availability of overexpression and deletion strains for almost all of the transcription factor genes in the fission yeast Schizosaccharomyces pombe provides a valuable resource to better investigate transcription factors using systematic genetics.

Non-Darwinian dynamics in therapy-induced cancer drug resistance.

The development of drug resistance, the prime cause of failure in cancer therapy, is commonly explained by the selection of resistant mutant cancer cells. However, dynamic non-genetic heterogeneity of clonal cell populations continuously produces metastable phenotypic variants (persisters), some of which represent stem-like states that confer resistance. Even without genetic mutations, Darwinian selection can expand these resistant variants, which would explain the invariably rapid emergence of stem-like resistant cells.

Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations.

Methods directly evaluating the hydration structure and thermodynamics of physiologically relevant cations (Na(+), K(+), Cl(-), etc.) have wide ranging applications in the fields of inorganic, physical, and biological chemistry. All-atom simulations based on accurate potential energy surfaces appear to offer a viable option for assessing the chemistry of ion solvation.

Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations.

Potentials routinely used in atomistic molecular dynamics simulations are not always suitable for modeling systems at coarse-grained resolution. For example, in the calculation of traditional torsion angle potentials, numerical instability is often encountered in the case of very flexible molecules. To improve the stability and accuracy of coarse-grained molecular dynamics simulations, we propose two approaches.

Inhibition of mammalian carbonic anhydrases I-XIV with grayanotoxin III: solution and in silico studies.

Grayanotoxin III (GTX3) was investigated for inhibition of all catalytically active mammalian carbonic anhydrase (CA, EC 4.2.1.

Computer simulations of the phase separation in model membranes.

We used computer simulations to investigate the properties of model lipid membranes with coexisting phases. This is relevant for understanding lipid-lipid interactions underlying lateral organization in biological membranes. Molecular dynamics simulations with the MARTINI coarse-grained force field were employed to study lipid bilayers -40 nm in lateral dimension on a 20 micros time scale.

Functional characterization of fission yeast transcription factors by overexpression analysis.

In Schizosaccharomyces pombe, over 90% of transcription factor genes are nonessential. Moreover, the majority do not exhibit significant growth defects under optimal conditions when deleted, complicating their functional characterization and target gene identification. Here, we systematically overexpressed 99 transcription factor genes with the nmt1 promoter and found that 64 transcription factor genes exhibited reduced fitness when ectopically expressed.

Atomistic Simulations of Wimley-White Pentapeptides: Sampling of Structure and Dynamics in Solution.

Wimley-White pentapeptides (Ac-WLXLL) can be used as a model system to study lipid-protein interactions as they bind to lipid/water interfaces, like many antimicrobial peptides, and thermodynamic experimental data on their interactions with lipids are available, making them useful for both force field and method testing and development. Here we present a detailed simulation study of Wimley-White (WW) peptides in bulk water to investigate sampling, conformations, and differences due to the different X residue with an eye to future simulations at the lipid/water interface where sampling problems so far have hindered free energy calculations to reproduce the experimental thermodynamic data. We investigate the conformational preferences and slowest relaxation time of WW peptides in bulk water by building Markov State Models (MSM) from Molecular Dynamics (MD) simulation data.

Free energy of WALP23 dimer association in DMPC, DPPC, and DOPC bilayers.

The MARTINI coarse-grained model is used to gain insight into the association of WALP23 helices in three different lipid membranes: DMPC, DPPC and DOPC. Potentials of mean force describing the association of two WALP23 helices embedded in different lipid bilayers indicate no barrier of association and a stabilization of more than 20 kJ mol(-1) of the associated state relative to the fully dissociated state. Association is strongest in DMPC, followed by DPPC and DOPC.

When peers are not peers and don't know it: The Dunning-Kruger effect and self-fulfilling prophecy in peer-review.

The fateful combination of (i) the Dunning-Kruger effect (ignorance of one's own ignorance) with (ii) the nonlinear dynamics of the echo-chamber between reviewers and editors fuels a self-reinforcing collective delusion system that sometimes spirals uncontrollably away from objectivity and truth. Escape from this subconscious meta-ignorance is a formidable challenge but if achieved will help correct a central deficit of the peer-review process that stifles innovation and paradigm shifts.

Role of protein matrix rigidity and local polarization effects in the monovalent cation selectivity of crystallographic sites in the Na-coupled aspartate transporter Glt(Ph).

We have studied Li(+)/Na(+)/K(+) selectivity of the bacterial aspartate transporter Glt(Ph) using all-atom molecular dynamics (MD) and free energy simulations (FES) to evaluate the role of different factors that control ion preferences of the binding sites identified in the crystallographic structure. The role of the bound ions in stabilizing the hairpin loop (HP2) by acting as an extracellular gate is discussed. Free energy simulations with classical and polarizable force-fields were used to characterize the role of the protein matrix, the site composition and the induced polarization in the stabilization of native and non-native cations, such as Li(+) and K(+), in the ion-binding sites of the transporter.

Improved Parameters for the Martini Coarse-Grained Protein Force Field.

The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too hydrophobic, and dimers formed by polar residues in apolar solvents did not bind strongly enough.

Deciphering the transcriptional-regulatory network of flocculation in Schizosaccharomyces pombe.

In the fission yeast Schizosaccharomyces pombe, the transcriptional-regulatory network that governs flocculation remains poorly understood. Here, we systematically screened an array of transcription factor deletion and overexpression strains for flocculation and performed microarray expression profiling and ChIP-chip analysis to identify the flocculin target genes. We identified five transcription factors that displayed novel roles in the activation or inhibition of flocculation (Rfl1, Adn2, Adn3, Sre2, and Yox1), in addition to the previously-known Mbx2, Cbf11, and Cbf12 regulators.

Asymptotic Expansion for Electrostatic Embedding Integrals in QM/MM Calculations.

In QM/MM studies with large MM regions, the calculation of electrostatic embedding integrals can become a computational bottleneck. To overcome this problem, an asymptotic expansion for nuclear attraction-type integrals is developed. As a result, the long-range interactions between the QM and MM atoms reduce to atom-centered multipole moment-like expansions.

Ion-controlled conformational dynamics in the outward-open transition from an occluded state of LeuT.

Neurotransmitter:sodium symporter (NSS) proteins are secondary Na(+)-driven active transporters that terminate neurotransmission by substrate uptake. Despite the availability of high-resolution crystal structures of a bacterial homolog of NSSs-Leucine Transporter (LeuT)-and extensive computational and experimental structure-function studies, unanswered questions remain regarding the transport mechanisms. We used microsecond atomistic molecular-dynamics (MD) simulations and free-energy computations to reveal ion-controlled conformational dynamics of LeuT in relation to binding affinity and selectivity of the more extracellularly positioned Na(+) binding site (Na1 site).

Molecular view of phase coexistence in lipid monolayers.

We used computer simulations to study the effect of phase separation on the properties of lipid monolayers. This is important for understanding the lipid-lipid interactions underlying lateral heterogeneity (rafts) in biological membranes and the role of domains in the regulation of surface tension by lung surfactant. Molecular dynamics simulations with the coarse-grained MARTINI force field were employed to model large length (~80 nm in lateral dimension) and time (tens of microseconds) scales.