pwc-archive/papers-with-abstracts huggingface dataset:
How the Avidity of Polymerase Binding to the -35/-10 Promoter Sites Affects Gene Expression
Authors: Tal Einav, Rob Phillips
Date: 2019-04-03 00:00:00

Although the key promoter elements necessary to drive transcription in Escherichia coli have long been understood, we still cannot predict the behavior of arbitrary novel promoters, hampering our ability to characterize the myriad of sequenced regulatory architectures as well as to design novel synthetic circuits. This work builds upon a beautiful recent experiment by Urtecho et al. who measured the gene expression of over 10,000 promoters spanning all possible combinations of a small set of regulatory elements. Using this data, we demonstrate that a central claim in energy matrix models of gene expression - that each promoter element contributes independently and additively to gene expression - contradicts experimental measurements. We propose that a key missing ingredient from such models is the avidity between the -35 and -10 RNA polymerase binding sites and develop what we call a refined energy matrix model that incorporates this effect. We show that this the refined energy matrix model can characterize the full suite of gene expression data and explore several applications of this framework, namely, how multivalent binding at the -35 and -10 sites can buffer RNAP kinetics against mutations and how promoters that bind overly tightly to RNA polymerase can inhibit gene expression. The success of our approach suggests that avidity represents a key physical principle governing the interaction of RNA polymerase to its promoter.
Diffusiophoresis in Cells: a General Non-Equilibrium, Non-Motor Mechanism for the Metabolism-Dependent Transport of Particles in Cells
Authors: Richard P. Sear
Date: 2019-01-03 00:00:00

The more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or down these gradients due to a mechanism called diffusiophoresis. I estimate that inside metabolically active cells, the dynamics of particles can be strongly accelerated by diffusiophoresis, provided that they are at least tens of nanometres across. The dynamics of smaller objects, such as single proteins are largely unaffected.
Further Thoughts on Abnormal Chromatin Configuration and Oncogenesis
Authors: Gao-De Li
Date: 2019-01-14 00:00:00

More than 30 years ago, we published a paper entitled as abnormal chromatin configuration and oncogenesis, which proposed the first hypothesis that links oncogenesis to abnormal three-dimensional (3D) genome structure. Recently, many studies have demonstrated that the 3D genome structure plays a major role in oncogenesis, which strongly supports our hypothesis. In this paper, further thoughts about our hypothesis is presented.
Boundary lipids of the nicotinic acetylcholine receptor: spontaneous partitioning via coarse-grained molecular dynamics simulation
Authors: Liam Sharp, Reza Salari, Grace Brannigan
Date: 2018-07-29 00:00:00

Reconstituted nicotinic acetylcholine receptors (nAChRs) exhibit significant gain-of-function upon addition of cholesterol to reconstitution mixtures, and cholesterol affects organization of nAChRs within domain-forming membranes, but whether nAChR partitions to cholesterol-rich liquid-ordered ("raft" or $l_o$) domains or cholesterol-poor liquid-disordered ($l_{do}$) domains is unknown. We use coarse-grained molecular dynamics simulations to observe spontaneous interactions of cholesterol, saturated lipids, and polyunsaturated (PUFA) lipids with nAChRs. In binary Dipalmitoylphosphatidylcholine:Cholesterol (DPPC:CHOL) mixtures, both CHOL and DPPC acyl chains were observed spontaneously entering deep "non-annular" cavities in the nAChR TMD, particularly at the subunit interface and the $\beta$ subunit center, facilitated by the low amino acid density in the cryo-EM structure of nAChR in a native membrane. Cholesterol was highly enriched in the annulus around the TMD, but this effect extended over (at most) 5-10\AA. In domain-forming ternary mixtures containing PUFAs, the presence of a single receptor did not significantly affect the likelihood of domain formation. nAChR partitioned to any cholesterol-poor $l_{do}$ domain that was present, regardless of whether the $l_{do}$ or $l_o$ domain lipids had PC or PE headgroups. Enrichment of PUFAs among boundary lipids was positively correlated with their propensity for demixing from cholesterol-rich phases. Long $n - 3$ chains (tested here with Docosahexaenoic Acid, DHA) were highly enriched in annular and non-annular embedded sites, partially displacing cholesterol and completely displacing DPPC, and occupying sites even deeper within the bundle. Shorter $n - 6$ chains were far less effective at displacing cholesterol from non-annular sites.
Non-Markovian intracellular transport with sub-diffusion and run-length dependent detachment rate
Authors: Nickolay Korabel, Thomas A. Waigh, Sergei Fedotov, Viki J. Allan
Date: 2018-11-04 00:00:00

Intracellular transport of organelles is fundamental to cell function and health. The mounting evidence suggests that this transport is in fact anomalous. However, the reasons for the anomaly is still under debate. We examined experimental trajectories of organelles inside a living cell and propose a mathematical model that describes the previously reported transition from sub-diffusive to super-diffusive motion. In order to explain super-diffusive behaviour at long times, we introduce non-Markovian detachment kinetics of the cargo: the rate of detachment is inversely proportional to the time since the last attachment. Recently, we observed the non-Markovian detachment rate experimentally in eukaryotic cells. Here we further discuss different scenarios of how this effective non-Markovian detachment rate could arise. The non-Markovian model is successful in simultaneously describing the time-averaged variance (the time-averaged mean squared displacement corrected for directed motion), the mean first passage time of trajectories and the multiple peaks observed in the distributions of cargo velocities. We argue that non-Markovian kinetics could be biologically beneficial compared to the Markovian kinetics commonly used for modelling, by increasing the average distance the cargoes travel when a microtubule is blocked by other filaments. In turn, sub-diffusion allows cargoes to reach neighbouring filaments with higher probability, which promotes active motion along the microtubules.
Universal kinetics for engagement of mechanosensing pathways in cell adhesion
Authors: Samuel Bell, Anna-Lena Redmann, Eugene M. Terentjev
Date: 2018-03-12 00:00:00

When plated onto substrates, cell morphology and even stem cell differentiation are influenced by the stiffness of their environment. Stiffer substrates give strongly spread (eventually polarized) cells with strong focal adhesions, and stress fibers; very soft substrates give a less developed cytoskeleton, and much lower cell spreading. The kinetics of this process of cell spreading is studied extensively, and important universal relationships are established on how the cell area grows with time. Here we study the population dynamics of spreading cells, investigating the characteristic processes involved in cell response to the substrate. We show that unlike the individual cell morphology, this population dynamics does not depend on the substrate stiffness. Instead, a strong activation temperature dependence is observed. Different cell lines on different substrates all have long-time statistics controlled by the thermal activation over a single energy barrier dG=19 kcal/mol, while the early-time kinetics follows a power law $t^5$. This implies that the rate of spreading depends on an internal process of adhesion-mechanosensing complex assembly and activation: the operational complex must have 5 component proteins, and the last process in the sequence (which we believe is the activation of focal adhesion kinase) is controlled by the binding energy dG.
Transport Facilitated by Rapid Binding to Elastic Tethers
Authors: Ben Fogelson, James P. Keener
Date: 2018-09-04 00:00:00

Diffusion in cell biology is important and complicated. Diffusing particles must contend with a complex environment as they make their way through the cell. We analyze a particular type of complexity that arises when diffusing particles reversibly bind to elastically tethered binding partners. Using asymptotic analysis, we derive effective equations for the transport of both single and multiple particles in the presence of such elastic tethers. We show that for the case of linear elasticity and simple binding kinetics, the elastic tethers have a weak hindering effect on particle motion when only one particle is present, while, remarkably, strongly enhancing particle motion when multiple particles are present. We give a physical interpretation of this result that suggests a similar effect may be present in other biological settings.
Reaction-diffusion kinetics on lattice at the microscopic scale
Authors: Wei-Xiang Chew, Kazunari Kaizu, Masaki Watabe, Sithi V. Muniandy, Koichi Takahashi, Satya N. V. Arjunan
Date: 2018-05-31 00:00:00

Lattice-based stochastic simulators are commonly used to study biological reaction-diffusion processes. Some of these schemes that are based on the reaction-diffusion master equation (RDME), can simulate for extended spatial and temporal scales but cannot directly account for the microscopic effects in the cell such as volume exclusion and diffusion-influenced reactions. Nonetheless, schemes based on the high-resolution microscopic lattice method (MLM) can directly simulate these effects by representing each finite-sized molecule explicitly as a random walker on fine lattice voxels. The theory and consistency of MLM in simulating diffusion-influenced reactions have not been clarified in detail. Here, we examine MLM in solving diffusion-influenced reactions in 3D space by employing the Spatiocyte simulation scheme. Applying the random walk theory, we construct the general theoretical framework underlying the method and obtain analytical expressions for the total rebinding probability and the effective reaction rate. By matching Collins-Kimball and lattice-based rate constants, we obtained the exact expressions to determine the reaction acceptance probability and voxel size. We found that the size of voxel should be about 2% larger than the molecule. MLM is validated by numerical simulations, showing good agreement with the off-lattice particle-based method, eGFRD. MLM run time is more than an order of magnitude faster than eGFRD when diffusing macromolecules with typical concentrations in the cell. MLM also showed good agreements with eGFRD and mean-field models in case studies of two basic motifs of intracellular signaling, the protein production-degradation process and the dual phosphorylation cycle. Moreover, when a reaction compartment is populated with volume-excluding obstacles, MLM captures the non-classical reaction kinetics caused by anomalous diffusion of reacting molecules.
Mechanisms of Protein Search for Targets on DNA: Theoretical Insights
Authors: Alexey A. Shvets, Maria P. Kochugaeva, Anatoly B. Kolomeisky
Date: 2018-08-03 00:00:00
Tasks: Specificity

Protein-DNA interactions are critical for the successful functioning of all natural systems. The key role in these interactions is played by processes of protein search for specific sites on DNA. Although it has been studied for many years, only recently microscopic aspects of these processes became more clear. In this work, we present a review on current theoretical understanding of the molecular mechanisms of the protein target search. A comprehensive discrete-state stochastic method to explain the dynamics of the protein search phenomena is introduced and explained. Our theoretical approach utilizes a first-passage analysis and it takes into account the most relevant physical-chemical processes. It is able to describe many fascinating features of the protein search, including unusually high effective association rates, high selectivity and specificity, and the robustness in the presence of crowders and sequence heterogeneity.
Curvature-sensitive kinesin binding can explain microtubule ring formation and reveals chaotic dynamics in a mathematical model
Authors: Simon P Pearce, Matthias Heil, Oliver E Jensen, Gareth W Jones, Andreas Prokop
Date: 2018-03-20 00:00:00

Microtubules are filamentous tubular protein polymers which are essential for a range of cellular behaviour, and are generally straight over micron length scales. However, in some gliding assays, where microtubules move over a carpet of molecular motors, individual microtubules can also form tight arcs or rings, even in the absence of crosslinking proteins. Understanding this phenomenon may provide important explanations for similar highly curved microtubules which can be found in nerve cells undergoing neurodegeneration. We propose a model for gliding assays where the kinesins moving the microtubules over the surface induce ring formation through differential binding, substantiated by recent findings that a mutant version of the motor protein kinesin applied in solution is able to lock-in microtubule curvature. For certain parameter regimes, our model predicts that both straight and curved microtubules can exist simultaneously as stable steady-states, as has been seen experimentally. Additionally, unsteady solutions are found, where a wave of differential binding propagates down the microtubule as it glides across the surface, which can lead to chaotic motion. Whilst this model explains two-dimensional microtubule behaviour in an experimental gliding assay, it has the potential to be adapted to explain pathological curling in nerve cells.
Non-associative learning in intra-cellular signaling networks
Authors: Tanmay Mitra, Shakti N. Menon, Sitabhra Sinha
Date: 2018-07-03 00:00:00

Nonlinear systems driven by recurrent signals are known to exhibit complex dynamical responses which, in the physiological context, can have important functional consequences. One of the simplest biological systems that is exposed to such repeated stimuli is the intra-cellular signaling network. In this paper we investigate the periodic activation of an evolutionarily conserved motif of this network, viz., the mitogen-activated protein kinase (MAPK) signaling cascade, with a train of pulses. The resulting response of the cascade, which shows integrative capability over several successive pulses, is characterized by complex adaptive behavior. These include aspects of non-associative learning, in particular, habituation and sensitization, which are observed in response to high- and low-frequency stimulation, respectively. In addition, the existence of a response threshold of the cascade, an apparent refractory behavior following stimulation with short inter-pulse interval, and an alternans-like response under certain conditions suggest an analogy with excitable media.
Nanopore occlusion: A biophysical mechanism for bipolar cancellation in cell membranes
Authors: Thiruvallur R. Gowrishankar, Julie V. Stern, Kyle C. Smith, James C. Weaver
Date: 2018-07-03 00:00:00

Extraordinarily large but short electric field pulses are reported by many experiments to cause bipolar cancellation (BPC). This unusual cell response occurs if a first pulse is followed by a second pulse with opposite polarity. Possibly universal, BPC presently lacks a mechanistic explanation. Multiple versions of the "standard model" of cell electroporation (EP) fail to account for BPC. Here we show, for the first time, how an extension of the standard model can account for a key experimental observation that essentially defines BPC: the amount of a tracer that enters a cell, and how tracer influx can be decreased by the second part of a bipolar pulse. The extended model can also account for the recovery of BPC wherein the extent of BPC is diminished if the spacing between the first and second pulses is increased. Our approach is reverse engineering, meaning that we identify and introduce an additional biophysical mechanism that allows pore transport to change. We hypothesize that occluding molecules from outside the membrane enter or relocate within a pore. Significantly, the additional mechanism is fundamental and general, involving a combination of partitioning and hindrance. Molecules near the membrane can enter pores to block transport of tracer molecules while still passing small ions (+/- 1) that govern electrical behavior. Accounting for such behavior requires an extension of the standard model.
Unveiling ADP-binding sites and channels in respiratory complexes: Validation of Murburn concept as a holistic explanation for oxidative phosphorylation
Authors: Kelath Murali Manoj, Abhinav Parashar
Date: 2018-06-06 00:00:00

Mitochondrial oxidative phosphorylation (mOxPhos) makes ATP, the energy currency of life. Chemiosmosis, a proton centric mechanism, advocates that Complex V harnesses a transmembrane potential (TMP) for ATP synthesis. This perception of cellular respiration requires oxygen to stay tethered at Complex IV (an association inhibited by cyanide) and diffusible reactive oxygen species (DROS) are considered wasteful and toxic products. With new mechanistic insights on heme and flavin enzymes, an oxygen or DROS centric explanation (called murburn concept) was recently proposed for mOxPhos. In the new mechanism, TMP is not directly harnessed, protons are a rate limiting reactant and DROS within matrix serve as the chemical coupling agents that directly link NADH oxidation with ATP synthesis. Herein, we report multiple ADP binding sites and solvent accessible DROS channels in respiratory proteins, which validate the oxygen or DROS centric power generation (ATP synthesis) system in mOxPhos. Since cyanide's heme binding Kd is high (mM), low doses (uM) of cyanide is lethal because cyanide disrupts DROS dynamics in mOxPhos. The critical study also provides comprehensive arguments against Mitchell's and Boyer's explanations and extensive support for murburn concept based holistic perspectives for mOxPhos.
Modeling of drug diffusion in a solid tumor leading to tumor cell death
Authors: Aminur Rahman, Souparno Ghosh, Ranadip Pal
Date: 2018-06-05 00:00:00

It has been shown recently that changing the fluidic properties of a drug can improve its efficacy in ablating solid tumors. We develop a modeling framework for tumor ablation, and present the simplest possible model for drug diffusion in a spherical tumor with leaky boundaries and assuming cell death eventually leads to ablation of that cell effectively making the two quantities numerically equivalent. The death of a cell after a given exposure time depends on both the concentration of the drug and the amount of oxygen available to the cell. Higher oxygen availability leads to cell death at lower drug concentrations. It can be assumed that a minimum concentration is required for a cell to die, effectively connecting diffusion with efficacy. The concentration threshold decreases as exposure time increases, which allows us to compute dose-response curves. Furthermore, these curves can be plotted at much finer time intervals compared to that of experiments, which is used to produce a dose-threshold-response surface giving an observer a complete picture of the drug's efficacy for an individual. In addition, since the diffusion, leak coefficients, and the availability of oxygen is different for different individuals and tumors, we produce artificial replication data through bootstrapping to simulate error. While the usual data-driven model with Sigmoidal curves use 12 free parameters, our mechanistic model only has two free parameters, allowing it to be open to scrutiny rather than forcing agreement with data. Even so, the simplest model in our framework, derived here, shows close agreement with the bootstrapped curves, and reproduces well established relations, such as Haber's rule.
Quantifying the Sensitivity of HIV-1 Viral Entry to Receptor and Coreceptor Expression
Authors: Bhaven Mistry, Maria R. D'Orsogna, Nicholas E. Webb, Benhur Lee, Tom Chou
Date: 2018-05-08 00:00:00
Tasks: Sensitivity

Infection by many viruses begins with fusion of viral and cellular lipid membranes, followed by entry of viral contents into the target cell and ultimately, after many biochemical steps, integration of viral DNA into that of the host cell. The early steps of membrane fusion and viral capsid entry are mediated by adsorption to the cell surface, and receptor and coreceptor binding. HIV-1 specifically targets CD4+ helper T-cells of the human immune system and binds to the receptor CD4 and coreceptor CCR5 before fusion is initiated. Previous experiments have been performed using a cell line (293-Affinofile) in which the expression of CD4 and CCR5 concentration were independently controlled. After exposure to HIV-1 of various strains, the resulting infectivity was measured through the fraction of infected cells. To design and evaluate the effectiveness of drug therapies that target the inhibition of the entry processes, an accurate functional relationship between the CD4/CCR5 concentrations and infectivity is desired in order to more quantitatively analyze experimental data. We propose three kinetic models describing the possible mechanistic processes involved in HIV entry and fit their predictions to infectivity measurements, contrasting and comparing different outcomes. Our approach allows interpretation of the clustering of infectivity of different strains of HIV-1 in the space of mechanistic kinetic parameters. Our model fitting also allows inference of nontrivial stoichiometries of receptor and coreceptor binding and provides a framework through which to quantitatively investigate the effectiveness of fusion inhibitors and neutralizing antibodies.
Metabolomic response of osteosarcoma cells to nanographene oxide-mediated hyperthermia
Authors: Monica Cicuendez, Joana Flores, Helena Oliveira, M. Teresa Portoles, Maria Vallet-Regi, Mercedes Vila, Lola F. Duarte
Date: 2021-03-24 00:00:00

Nanographene oxide (nGO)-mediated hyperthermia has been increasingly investigated as a localised, minimally invasive anticancer therapeutic approach. Near InfraRed (NIR) light irradiation for inducing hyperthermia is particularly attractive, because biological systems mostly lack chromophores that absorb in this spectral window, facilitating the selective heating and destruction of cells which have internalized the NIR absorbing-nanomaterials. However, little is known about biological effects accompanying nGO-mediated hyperthermiaat cellular and molecular levels.In this work, well-characterised pegylatednGOsheets with an hydrodynamic size of 300 nm were incubated with human Saos-2 osteosarcoma cells for 24h and their incorporation verified by flow cytometry and confocal microscopy. No effect on cell viability was observed after nGO incorporation by Saos-2 cells. However, a proliferation delay was observed due to the presence of nGO sheets in the cytoplasm.1H NMR metabolomicswas employed to screen for changes in the metabolic profile of cells, as this could help to improve understanding of celular responses to nanomaterials and provide new endpoint markers of effect.Cells incorporating nGO sheets showed noticeable changes in 10 metabolites compared to control cells, including decreased levels of several amino acids, taurine and creatine and increased levels of phosphocholine and uridine/adenosine nucleotides. After NIR irradiation, cells showed decreases in glutamate and uridine nulceotides, together with increases in glycerophosphocholine and adenosine monophosphate. Overall, this study has shown that the celular metabolome sensitively responded to nGO exposure and nGO-mediated hyperthermia and that NMR metabolomics is a powerful tool toinvestigate treatment responses.