Coulomb interactions between cytoplasmic electric fields and phosphorylated messenger proteins optimize information flow in cells

Modeling non-genetic information dynamics in cells using reservoir computing

Virtually all cells use energy-driven, ion-specific membrane pumps to maintain large transmembrane gradients of Na+, K+, Cl-, Mg++, and Ca++, but the corresponding evolutionary benefit remains unclear. We propose that these gradients enable a dynamic and versatile biological system that acquires, analyzes, and responds to environmental information. We hypothesize that environmental signals are transmitted into the cell by ion fluxes along pre-existing gradients through gated ion-specific membrane channels. The consequent changes in cytoplasmic ion concentration can generate a local response or orchestrate global/regional cellular dynamics through wire-like ion fluxes along pre-existing and self-assembling cytoskeleton to engage the endoplasmic reticulum, mitochondria, and nucleus.

The Sub-Molecular and Atomic Theory of Cancer Beginning: The Role of Mitochondria

Life as we know it is made of strict interaction of atom, metabolism, and genetics, made around the chemistry of the most common elements of the universe: hydrogen, oxygen, nitrogen, sulfur, phosphorus, and carbon. The interaction of atomic, metabolic, and genetic cycles results in the organization and de-organization of chemical information of what we consider living entities, including cancer cells. In order to approach the problem of the origin of cancer, it is therefore reasonable to start from the assumption that the atomic structure, metabolism, and genetics of cancer cells share a common frame with prokaryotic mitochondria, embedded in conditions favorable for the onset of both. Despite years of research, cancer in its general acceptation remains enigmatic. Despite the increasing efforts to investigate the complexity of tumorigenesis, complementing the research on genetic and biochemical changes, researchers face insurmountable limitations due to the huge presence of variabilities in cancer and metastatic behavior. The atomic level of all biological activities it seems confirmed the electron behavior, especially within the mitochondria. The electron spin may be considered a key factor in basic biological processes defining the structure, reactivity, spectroscopic, and magnetic properties of a molecule. The use of magnetic fields (MF) has allowed a better understanding of the grade of influence on different biological systems, clarifying the multiple effects on electron behavior and consequently on cellular changes. Scientific advances focused on the mechanics of the cytoskeleton and the cellular microenvironment through mechanical properties of the cell nucleus and its connection to the cytoskeleton play a major role in cancer metastasis and progression. Here, we present a hypothesis regarding the changes that take place at the atomic and metabolic levels within the human mitochondria and the modifications that probably drive it in becoming cancer cell. We propose how atomic and metabolic changes in structure and composition could be considered the unintelligible reason of many cancers’ invulnerability, as it can modulate nuclear mechanics and promote metastatic processes. Improved insights into this interplay between this sub-molecular organized dynamic structure, nuclear mechanics, and metastatic progression may have powerful implications in cancer diagnostics and therapy disclosing innovation in targets of cancer cell invasion.

Applied electric fields suppress osimertinib-induced cytotoxicity via inhibiting FOXO3a nuclear translocation through AKT activation

Osimertinib is a third-generation epidermal growth factor receptor tyrosine kinase inhibitor against T790M-mutant non-small cell lung cancer (NSCLC). Acquired resistance to osimertinib is a growing clinical challenge that is not fully understood. Endogenous electric fields (EFs), components of the tumor microenvironment, are associated with cancer cell migration and proliferation. However, the impact of EFs on drug efficiency has not been studied. In this study, we observed that EFs counteracted the effects of osimertinib. EFs of 100 mV/mm suppressed osimertinib-induced cell death and promoted cell proliferation. Transcriptional analysis revealed that the expression pattern induced by osimertinib was altered by EFs stimulation. KEGG analysis showed that differential expression genes were mostly enriched in PI3K-AKT pathway. Then, we found that osimertinib inhibited AKT phosphorylation, while EFs stimulation resulted in significant activation of AKT, which could override the effects generated by osimertinib. Importantly, pharmacological inhibition of PI3K/AKT by LY294002 diminished EF-induced activation of AKT and restored the cytotoxicity of osimertinib suppressed by EFs, which proved that AKT activation was essential for EFs to attenuate the efficacy of osimertinib. Furthermore, activation of AKT by EFs led to phosphorylation of forkhead box O3a (FOXO3a), and reduction in nuclear translocation of FOXO3a induced by osimertinib, resulting in decreased expression of Bim and attenuated cytotoxicity of osimertinib. Taken together, we demonstrated that EFs suppressed the antitumor activity of osimertinib through AKT/FOXO3a/Bim pathway, and combination of PI3K/AKT inhibitor with osimertinib counteracted the effects of EFs. Our findings provided preliminary data for therapeutic strategies to enhance osimertinib efficacy in NSCLC patients.

The Role of Cell Membrane Information Reception, Processing, and Communication in the Structure and Function of Multicellular Tissue

Investigations of information dynamics in eukaryotic cells focus almost exclusively on heritable information in the genome. Gene networks are modeled as “central processors” that receive, analyze, and respond to intracellular and extracellular signals with the nucleus described as a cell’s control center. Here, we present a model in which cellular information is a distributed system that includes non-genomic information processing in the cell membrane that may quantitatively exceed that of the genome. Within this model, the nucleus largely acts a source of macromolecules and processes information needed to synchronize their production with temporal variations in demand. However, the nucleus cannot produce microsecond responses to acute, life-threatening perturbations and cannot spatially resolve incoming signals or direct macromolecules to the cellular regions where they are needed. In contrast, the cell membrane, as the interface with its environment, can rapidly detect, process, and respond to external threats and opportunities through the large amounts of potential information encoded within the transmembrane ion gradient. Our model proposes environmental information is detected by specialized protein gates within ion-specific transmembrane channels. When the gate receives a specific environmental signal, the ion channel opens and the received information is communicated into the cell via flow of a specific ion species (i.e., K⁺, Na⁺, Cl⁻, Ca²⁺, Mg²⁺) along electrochemical gradients. The fluctuation of an ion concentration within the cytoplasm adjacent to the membrane channel can elicit an immediate, local response by altering the location and function of peripheral membrane proteins. Signals that affect a larger surface area of the cell membrane and/or persist over a prolonged time period will produce similarly cytoplasmic changes on larger spatial and time scales. We propose that as the amplitude, spatial extent, and duration of changes in cytoplasmic ion concentrations increase, the information can be communicated to the nucleus and other intracellular structure through ion flows along elements of the cytoskeleton to the centrosome (via microtubules) or proteins in the nuclear membrane (via microfilaments). These dynamics add spatial and temporal context to the more well-recognized information communication from the cell membrane to the nucleus following ligand binding to membrane receptors. Here, the signal is transmitted and amplified through transduction by the canonical molecular (e.g., Mitogen Activated Protein Kinases (MAPK) pathways. Cytoplasmic diffusion allows this information to be broadly distributed to intracellular organelles but at the cost of loss of spatial and temporal information also contained in ligand binding.

Ferritin and neuromelanin "quantum dot" array structures in dopamine neurons of the substantia nigra pars compacta and norepinephrine neurons of the locus coeruleus

In this review, the author shows that ferritin has documented quantum dot material properties that have been reported in numerous independent studies, and can enable quantum mechanical electron transport over substantial distances. In addition, neuromelanin is a pi-conjugated polymer, and quantum dot/pi-conjugated polymer combinations have been reported in numerous independent studies to facilitate electron transport for solar photovoltaic and other applications. Both ferritin and neuromelanin are present in large quantities in the dopamine neurons of the substantia nigra pars compactaand the norepinephrine neurons of the locus coeruleus. The unique structure of subgroups of these neurons that have a large number of axon branches and synapses may have evolved to take advantage of this electron transport mechanism, if it is present, such as to coordinate conscious action, or for other purposes. Independent clinical and laboratory studies are also reviewed that corroborate this theory of coordinated action in these neuron groups. Research to validate the theory using charge transport measurements, materials characterization, existing fluorescent probe material and reaction time testing is proposed.

Biological wires, communication systems, and implications for disease

Microtubules, actin, and collagen are macromolecular structures that compose a large percentage of the proteins in the human body, helping form and maintain both intracellular and extracellular structure. They are biological wires and are structurally connected through various other proteins. Microtubules (MTs) have been theorized to be involved in classical and quantum information processing, and evidence continues to suggest possible semiconduction through MTs. The previous Dendritic Cytoskeleton Information Processing Model has hypothesized how MTs and actin form a communication network in neurons. Here, we review information transfer possibilities involving MTs, actin, and collagen, and the evidence of an organism-wide high-speed communication network that may regulate morphogenesis and cellular proliferation. The direct and indirect evidence in support of this hypothesis, and implications for chronic diseases such as cancer and neurodegenerative diseases are discussed.

Principle of maximum Fisher information from Hardy's axioms applied to statistical systems

Consider a finite-sized, multidimensional system in parameter state a. The system is either at statistical equilibrium or general nonequilibrium, and may obey either classical or quantum physics. L. Hardy's mathematical axioms provide a basis for the physics obeyed by any such system. One axiom is that the number N of distinguishable states a in the system obeys N=max. This assumes that N is known as deterministic prior knowledge. However, most observed systems suffer statistical fluctuations, for which N is therefore only known approximately. Then what happens if the scope of the axiom N=max is extended to include such observed systems? It is found that the state a of the system must obey a principle of maximum Fisher information, I=I(max). This is important because many physical laws have been derived, assuming as a working hypothesis that I=I(max). These derivations include uses of the principle of extreme physical information (EPI). Examples of such derivations were of the De Broglie wave hypothesis, quantum wave equations, Maxwell's equations, new laws of biology (e.g., of Coulomb force-directed cell development and of in situ cancer growth), and new laws of economic fluctuation and investment. That the principle I=I(max) itself derives from suitably extended Hardy axioms thereby eliminates its need to be assumed in these derivations. Thus, uses of I=I(max) and EPI express physics at its most fundamental level, its axiomatic basis in math.

Cell development obeys maximum Fisher information

Eukaryotic cell development has been optimized by natural selection to obey maximal intracellular flux of messenger proteins. This, in turn, implies maximum Fisher information on angular position about a target nuclear pore complex (NPR). The cell is simply modeled as spherical, with cell membrane (CM) diameter 10 micrometer and concentric nuclear membrane (NM) diameter 6 micrometer. The NM contains approximately 3000 nuclear pore complexes (NPCs). Development requires messenger ligands to travel from the CM-NPC-DNA target binding sites. Ligands acquire negative charge by phosphorylation, passing through the cytoplasm over Newtonian trajectories toward positively charged NPCs (utilizing positive nuclear localization sequences). The CM-NPC channel obeys maximized mean protein flux F and Fisher information I at the NPC. Therefore the first-order change in I = 0. But also, the 2nd-order change in I is likewise close to zero, indicating significant stability to environmental perturbations. Many predictions are confirmed, including the dominance of protein pathways of from 1-4 proteins, a 4 nm size for the EGFR protein and the flux value F approximately 10(16) proteins/m2-s. After entering the nucleus, each protein ultimately delivers its ligand information to a DNA target site with maximum probability, i.e. maximum Kullback-Liebler entropy H(KL). In a smoothness limit H(KL) --> I(DNA)/2, so that the total CM-NPC-DNA channel obeys maximum Fisher I. It is also shown that such maximum information --> a cell state far from thermodynamic equilibrium, one condition for life.

Cytoplasmic electric fields and electroosmosis: possible solution for the paradoxes of the intracellular transport of biomolecules

The objective of the paper is to show that electroosmotic flow might play an important role in the intracellular transport of biomolecules. The paper presents two mathematical models describing the role of electroosmosis in the transport of the negatively charged messenger proteins to the negatively charged nucleus and in the recovery of the fluorescence after photobleaching. The parameters of the models were derived from the extensive review of the literature data. Computer simulations were performed within the COMSOL 4.2a software environment. The first model demonstrated that the presence of electroosmosis might intensify the flux of messenger proteins to the nucleus and allow the efficient transport of the negatively charged phosphorylated messenger proteins against the electrostatic repulsion of the negatively charged nucleus. The second model revealed that the presence of the electroosmotic flow made the time of fluorescence recovery dependent on the position of the bleaching spot relative to cellular membrane. The magnitude of the electroosmotic flow effect was shown to be quite substantial, i.e. increasing the flux of the messengers onto the nucleus up to 4-fold relative to pure diffusion and resulting in the up to 3-fold change in the values of fluorescence recovery time, and therefore the apparent diffusion coefficient determined from the fluorescence recovery after photobleaching experiments. Based on the results of the modeling and on the universal nature of the electroosmotic flow, the potential wider implications of electroosmotic flow in the intracellular and extracellular biological processes are discussed. Both models are available for download at ModelDB.

The critical roles of information and nonequilibrium thermodynamics in evolution of living systems

Living cells are spatially bounded, low entropy systems that, although far from thermodynamic equilibrium, have persisted for billions of years. Schrödinger, Prigogine, and others explored the physical principles of living systems primarily in terms of the thermodynamics of order, energy, and entropy. This provided valuable insights, but not a comprehensive model. We propose the first principles of living systems must include: (1) Information dynamics, which permits conversion of energy to order through synthesis of specific and reproducible, structurally-ordered components; and (2) Nonequilibrium thermodynamics, which generate Darwinian forces that optimize the system.Living systems are fundamentally unstable because they exist far from thermodynamic equilibrium, but this apparently precarious state allows critical response that includes: (1) Feedback so that loss of order due to environmental perturbations generate information that initiates a corresponding response to restore baseline state. (2) Death due to a return to thermodynamic equilibrium to rapidly eliminate systems that cannot maintain order in local conditions. (3) Mitosis that rewards very successful systems, even when they attain order that is too high to be sustainable by environmental energy, by dividing so that each daughter cell has a much smaller energy requirement. Thus, nonequilibrium thermodynamics are ultimately responsible for Darwinian forces that optimize system dynamics, conferring robustness sufficient to allow continuous existence of living systems over billions of years.

Intracellular electric field and pH optimize protein localization and movement

Mammalian cell function requires timely and accurate transmission of information from the cell membrane (CM) to the nucleus (N). These pathways have been intensively investigated and many critical components and interactions have been identified. However, the physical forces that control movement of these proteins have received scant attention. Thus, transduction pathways are typically presented schematically with little regard to spatial constraints that might affect the underlying dynamics necessary for protein-protein interactions and molecular movement from the CM to the N. We propose messenger protein localization and movements are highly regulated and governed by Coulomb interactions between: 1. A recently discovered, radially directed E-field from the NM into the CM and 2. Net protein charge determined by its isoelectric point, phosphorylation state, and the cytosolic pH. These interactions, which are widely applied in elecrophoresis, provide a previously unknown mechanism for localization of messenger proteins within the cytoplasm as well as rapid shuttling between the CM and N. Here we show these dynamics optimize the speed, accuracy and efficiency of transduction pathways even allowing measurement of the location and timing of ligand binding at the CM –previously unknown components of intracellular information flow that are, nevertheless, likely necessary for detecting spatial gradients and temporal fluctuations in ligand concentrations within the environment. The model has been applied to the RAF-MEK-ERK pathway and scaffolding protein KSR1 using computer simulations and in-vitro experiments. The computer simulations predicted distinct distributions of phosphorylated and unphosphorylated components of this transduction pathway which were experimentally confirmed in normal breast epithelial cells (HMEC).

Order in a multidimensional system

We show that any convex K-dimensional system has a level of order R that is proportional to its level of Fisher information I. The proportionality constant is 1/8 the square of the longest chord connecting two surface points of the system. This result follows solely from the requirement that R decrease under small perturbations caused by a coarse graining of the system. The form for R is generally unitless, allowing the order for different phenomena, or different representations (e.g., using time vs frequency) of a given phenomenom, to be compared objectively. Order R is also invariant to uniform magnification of the system. The monotonic contraction properties of R and I define an arrow of time and imply that they are entropies, in addition to their usual status as informations. This also removes the need for data, and therefore an observer, in derivations of nonparticipatory phenomena that utilize I. Simple graphical examples of the new order measure show that it measures as well the level of "complexity" in the system. Finally, an application to cell growth during enforced distortion shows that a single hydrocarbon chain can be distorted into a membrane having equal order or complexity. Such membranes are prime constituents of living cells.