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At least 55 records · Page 3Linked to original sources

Spreading of EGF Receptor Activity into EGF-free Regions and Molecular Therapies of Cancer

The primary activation of the epidermal growth factor receptor (EGFR) has become a prominent target for molecular therapies against several forms of cancer. But despite considerable progress during the last years, many of its aspects remain poorly understood. Experiments on lateral spreading of receptor activity into ligand-free regions challenge the current standard models of EGFR activation. Here, we propose and study a theoretical model, which explains spreading into ligand-free regions without introducing any new, unknown kinetic parameters. The model exhibits bistability of activity, induced by a generic reaction mechanism, which consists of activation via dimerization and deactivation via a Michaelis-Menten reaction. It possesses slow propagating front solutions and faster initial transients. We analyze relevant experiments and find that they are in quantitative accordance with the fast initial modes of spreading, but not with the slow propagating front. We point out that lateral spreading of activity is linked to pathological levels of persistent receptor activity as observed in cancer cells and exemplify uses of this link for the design and quick evaluation of molecular therapies targeting primary activation of EGFR.

q-bio.MN↗

Surfing at the wave fronts: the bidirectional movement of cargo particles driven by molecular motors

The collective behavior of molecular motor proteins have been investigated in the literature using models to describe the long-time dynamics of a unidimensional continuum motor distribution. Here, we consider the phenomena related to the transport of particles (vesicles, organelles, virus, etc) in the realm of these continuum motor systems. We argue that cargo movement may result from its ability to perturb the existing motor distribution and to surf at the resulting shock waves separating regions of different motor densities within the transient regime. In this case, the observed bidirectionality of cargo movement is naturally associated with reversals of shocks directions. Comparison of the quantitative results predicted by this model with available data for cargo velocity allows us to suggest that geometrical characteristics of the transported particle shall determine the extension and intensity of the perturbation it produces and thus, its dynamics. Possible implications of these ideas to virus movement at the cell body are discussed in connection with their distinguished morphological characteristics. Key words: collective effects of molecular motors; cargo transport; non-linear partial differential equations; shock waves.

q-bio.SC↗

Reverse Engineering of Proteasomal Translocation Rates

We address the problem of proteasomal protein translocation and introduce a new stochastic model of the proteasomal digestion (cleavage) of proteins. In this model we account for the protein translocation and the positioning of cleavage sites of a proteasome from first principles. We show by test examples and by processing experimental data that our model allows reconstruction of the translocation and cleavage rates from mass spectroscopy data on digestion patterns and can be used to investigate the properties of transport in different experimental set-ups. Detailed investigation with this model will enable theoretical quantitative prediction of the proteasomal activity.

q-bio.OT↗

Conformation of single-stranded RNA in a virus capsid: implications of dimensional reduction

The statistical mechanics of a treelike polymer in a confining volume is relevant to the packaging of the genome in RNA viruses. Making use of the mapping of the grand partition function of this system onto the statistical mechanics of a hard-core gas in two fewer spatial dimensions and of techniques developed for the evaluation of the equilibrium properties of a one-dimensional hard rod gas, we show how it is possible to determine the density and other key properties of a collection of rooted excluded-volume tress confined between two walls, both in the absence and in the presence of a one-dimensional external potential. We find, somewhat surprisingly, that in the case of key quantities, the statistical mechanics of the excluded volume, randomly branched polymer map exactly into corresponding problems for an unrestricted linear polymer.

cond-mat.stat-mech↗

Macro- and Microscopic Self-Similarity in Neuro- and Psycho-Dynamics

The unique Hamiltonian description of neuro- and psycho-dynamics at the macroscopic, classical, inter-neuronal level of brain's neural networks, and microscopic, quantum, intra-neuronal level of brain's microtubules, is presented in the form of open Liouville equations. This implies the arrow of time in both neuro- and psycho-dynamic processes and shows the existence of the formal neuro-biological space-time self-similarity. Keywords: Neuro- and psycho-dynamics, Brain microtubules, Hamiltonian and Liouville dynamics, Neuro-biological self-similarity

q-bio.NC↗

Shuttle-mediated proton pumping across the inner mitochondrial membrane

Shuttle-assisted charge transfer is pivotal for the efficient energy transduction from the food-stuff electrons to protons in the respiratory chain of animal cells and bacteria. The respiratory chain consists of four metalloprotein Complexes (I-IV) embedded in the inner membrane of a mitochondrion. Three of these complexes pump protons across the membrane, fuelled by the energy of food-stuff electrons. Despite extensive biochemical and biophysical studies, the physical mechanism of this proton pumping is still not well understood. Here we present a nanoelectromechanical model of the electron-driven proton pump related to the second loop of the respiratory chain, where a lipid-soluble ubiquinone molecule shuttles between the Complex I and Complex III, carrying two electrons and two protons. We show that the energy of electrons can be converted to the transmembrane proton potential gradient via the electrostatic interaction between electrons and protons on the shuttle. We find that the system can operate either as a proton pump, or, in the reverse regime, as an electron pump. For membranes with various viscosities, we demonstrate that the uphill proton current peaks near the body temperature $T \approx 37 ^{\circ}$C.

cond-mat.other↗

Osmotic pressure: resisting or promoting DNA ejection from phage

Recent in vitro experiments have shown that DNA ejection from bacteriophage can be partially stopped by surrounding osmotic pressure when ejected DNA is digested by DNase I on the course of ejection. We argue in this work by combination of experimental techniques (osmotic suppression without DNaseI monitored by UV absorbance, pulse-field electrophoresis, and cryo-EM visualization) and simple scaling modeling that intact genome (i.e. undigested) ejection in a crowded environment is, on the contrary, enhanced or eventually complete with the help of a pulling force resulting from DNA condensation induced by the osmotic stress itself. This demonstrates that in vivo, the osmotically stressed cell cytoplasm will promote phage DNA ejection rather than resisting it. The further addition of DNA-binding proteins under crowding conditions is shown to enhance the extent of ejection. We also found some optimal crowding conditions for which DNA content remaining in the capsid upon ejection is maximum, which correlates well with the optimal conditions of maximum DNA packaging efficiency into viral capsids observed almost 20 years ago. Biological consequences of this finding are discussed.

physics.bio-ph↗

Traffic by small teams of molecular motors

Molecular motors transport various cargos along cytoskeletal filaments, analogous to trucks on roads. In contrast to vehicles, however, molecular motors do not work alone but in small teams. We describe a simple model for the transport of a cargo by one team of motors and by two teams of motors, which walk into opposite directions. The cooperation of one team of motors generates long-range transport, which we observed experimentally in vitro. Transport by two teams of motors leads to a variety of bidirectional motility behaviour and to dynamic instabilities reminiscent of spontaneous symmetry breaking. We also discuss how cargo transport by teams of motors allows the cell to generate robust long-range bidirectional transport.

cond-mat.stat-mech↗

Cyclooxygenase inhibition in ischemic brain injury

Neuroinflammation is one of the key pathological events involved in the progression of brain damage caused by cerebral ischemia. Metabolism of arachidonic acid through cyclooxygenase (COX) enzymes is known to be actively involved in the neuroinflammatory events leading to neuronal death after ischemia. Two isoforms of COX, termed COX-1 and COX-2, have been identified. Unlike COX-1, COX-2 expression is dramatically induced by ischemia and appears to be an effector of tissue damage. This review article will focus specifically on the involvement of COX isozymes in brain ischemia. We will discuss issues related to the biochemistry and selective pharmacological inhibition of COX enzymes, and further refer to their expression in the brain under normal conditions and following excitotoxicity and ischemic cerebral injury. We will review present knowledge of the relative contribution of each COX isoform to the brain ischemic pathology, based on data from investigations utilizing selective COX-1/COX-2 inhibitors and genetic knockout mouse models. The mechanisms of neurotoxicity associated with increased COX activity after ischemia will also be examined. Finally, we will provide a critical evaluation of the therapeutic potential of COX inhibitors in cerebral ischemia and discuss new targets downstream of COX with potential neuroprotective ability.

q-bio.TO↗

Consistency Principle in Biological Dynamical Systems

We propose a principle of consistency between different hierarchical levels of biological systems. Given a consistency between molecule replication and cell reproduction, universal statistical laws on cellular chemical abundances are derived and confirmed experimentally. They include a power law distribution of gene expressions, a lognormal distribution of cellular chemical abundances over cells, and embedding of the power law into the network connectivity distribution. Second, given a consistency between genotype and phenotype, a general relationship between phenotype fluctuations by genetic variation and isogenic phenotypic fluctuation by developmental noise is derived. Third, we discuss the chaos mechanism for stem cell differentiation with autonomous regulation, resulting from a consistency between cell reproduction and growth of the cell ensemble.

q-bio.CB↗

Fluids as Dynamic Templates for Cytoskeletal Proteins in Plant Cells

The Dynamic Template model of biological cell membranes and the cytoplasm as spatially organised fluid layers is extended to plant cells, and is shown to offer a feasible shear driven mechanism for the co-alignment of internal and external fibres observed during growth and tropic responses

physics.gen-ph↗

Resource Letter: Bio-molecular Nano-machines: where Physics, Chemistry, Biology and Technology meet

Cell is the structural and functional unit of life. This Resource Letter serves as a guide to the literature on nano-machines which drive not only intracellular movements, but also motility of the cell. These machines are usually proteins or macromolecular assemblies which require appropriate fuel for their operations. Although, traditionally, these machines were subjects of investigation in biology and biochemistry, increasing use of the concepts and techniques of physics in recent years have contributed to the quantitative understanding of the fundamental principles underlying their operational mechanisms. The possibility of exploiting these principles for the design and control of artificial nano-machines has opened up a new frontier in the bottom-up approach to nano-technology.

physics.bio-ph↗

Geometrical Bioelectrodynamics

This paper proposes rigorous geometrical treatment of bioelectrodynamics, underpinning two fast-growing biomedical research fields: bioelectromagnetism, which deals with the ability of life to produce its own electromagnetism, and bioelectromagnetics, which deals with the effect on life from external electromagnetism. Keywords: Bioelectrodynamics, exterior geometrical machinery, Dirac-Feynman quantum electrodynamics, functional electrical stimulation

q-bio.QM↗

Power-law scaling in protein synthesis of a stochastic regulon

We investigate the protein expression pattern of the lamB gene in Escherichia coli LE392. The gene product LamB is an important membrane protein for maltose transport into cells but it is also exploited by bacteriophage lambda for infection. Although our bacterial population is clonal, stochastic gene expression leads to a majority population with a large receptor number and a minority population with a small receptor number. We find that the LamB receptor distribution p(n) of the small-n population is scale invariant with the exponent depending on growth conditions. A heuristic model is proposed that relates the observed exponent to the protein production rate.

q-bio.CB↗

Peptide strings clues to the genesis and treatment of rheumatoid arthritis: rebuilding self-protective immunity amid fungal ruins

A recent application of the peptide strings concept has yielded novel perceptions on cell growth regulation, for instance that of oncoprotein metastasis. Here, this interdisciplinary approach at the boundary between physics and biology has been applied to gain a more profound insight into rheumatoid arthritis. As a result of the present investigation, this disease could be viewed as due to a metabolic dysregulation/syndrome-associated breakdown in the immunoglobulin A-based surveillance of the potentially pathogenic fungus Candida albicans that subsequently engenders a widespread self-destruction through cross-reactive auto-epitopes, ultimately amounting to the systemic predominance of a pro-inflammatory peptide string. Its therapeutic counterpart equally proposed in this report might serve as a model for future strategies against autoimmunity.

q-bio.SC↗

Can entropy save bacteria?

This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the organization of two athermal chains confined in a closed geometry characterized by two length scales (length and width). When applied to rod-shaped bacteria such as Escherichia coli, this phase diagram predicts that, despite strong confinement, duplicated chromosomes will demix, i.e., there exists a primordial physical driving force for chromosome segregation. The author discusses segregation of duplicating chromosomes using the concentric-shell model, which predicts that newly synthesized DNA will be found in the periphery of the chromosome during replication. In contrast to chromosomes, these results suggest that most plasmids will be randomly distributed inside the cell because of their small sizes. An active partitioning system is therefore required for accurate segregation of low-copy number plasmids. Implications of these results are also sketched, e.g., on the role of proteins, segregation mechanisms for bacteria of diverse shapes, cell cycle of an artificial cell, and evolution.

q-bio.SC↗

Minimal models for proteins and RNA: From folding to function

We present a panoramic view of the utility of coarse-grained (CG) models to study folding and functions of proteins and RNA. Drawing largely on the methods developed in our group over the last twenty years, we describe a number of key applications ranging from folding of proteins with disulfide bonds to functions of molecular machines. After presenting the theoretical basis that justifies the use of CG models, we explore the biophysical basis for the emergence of a finite number of folds from lattice models. The lattice model simulations of approach to the folded state show that non-native interactions are relevant only early in the folding process - a finding that rationalizes the success of structure-based models that emphasize native interactions. Applications of off-lattice $C_α$ and models that explicitly consider side chains ($C_α$-SCM) to folding of $β$-hairpin and effects of macromolecular crowding are briefly discussed. Successful application of a new class of off-lattice model, referred to as the Self-Organized Polymer (SOP), is shown by describing the response of Green Fluorescent Protein (GFP) to mechanical force. The utility of the SOP model is further illustrated by applications that clarify the functions of the chaperonin GroEL and motion of the molecular motor kinesin. We also present two distinct models for RNA, namely, the Three Site Interaction (TIS) model and the SOP model, that probe forced unfolding and force quench refolding of a simple hairpin and {\it Azoarcus} ribozyme. The predictions based on the SOP model show that force-induced unfolding pathways of the ribozyme can be dramatically changed by varying the loading rate. We conclude with a discussion of future prospects for the use of coarse-grained models in addressing problems of outstanding interest in biology.

q-bio.BM↗