Transcriptional drift in aging cells: A global decontroller.

As cells age, they undergo a remarkable global change: In transcriptional drift, hundreds of genes become overexpressed while hundreds of others become underexpressed. Using archetype modeling and Gene Ontology analysis on data from aging worms, we find that the up-regulated genes code for sensory proteins upstream of stress responses and down-regulated genes are growth- and metabolism-related. We observe similar trends within human fibroblasts, suggesting that this process is conserved in higher organisms.

Transcriptional drift in aging cells: A global de-controller.

As cells age, they undergo a remarkable global change: In , hundreds of genes become overexpressed while hundreds of others become underexpressed. Using archetype modeling and Gene Ontology analysis on data from aging worms, we find that the upregulated genes code for sensory proteins upstream of stress responses and downregulated genes are growth- and metabolism-related. We propose a simple mechanistic model for how such global coordination of multi-protein expression levels may be achieved by the binding of a single ligand that concentrates with age.

Proteostasis is adaptive: Balancing chaperone holdases against foldases.

Because a cell must adapt to different stresses and growth rates, its proteostasis system must too. How do cells detect and adjust proteome folding to different conditions? Here, we explore a biophysical cost-benefit principle, namely that the cell should keep its proteome as folded as possible at the minimum possible energy cost. This can be achieved by differential expression of chaperones-balancing foldases (which accelerate folding) against holdases (which act as parking spots).

Proteostasis collapse is a driver of cell aging and death.

What molecular processes drive cell aging and death? Here, we model how proteostasis-i.e., the folding, chaperoning, and maintenance of protein function-collapses with age from slowed translation and cumulative oxidative damage.

How Do Chaperones Protect a Cell's Proteins from Oxidative Damage?

The accumulation of protein damage in aging organisms is thought to contribute to many aging-related diseases. Yet the properties determining which proteins are most susceptible remain poorly understood. Are certain conformations more vulnerable? Which chaperones are the main guardians? We address these questions with a system-wide model of E.

Why Do Fast-Growing Bacteria Enter Overflow Metabolism? Testing the Membrane Real Estate Hypothesis.

Bacteria and other cells show a puzzling behavior. At high growth rates, E. coli switch from respiration (which is ATP-efficient) to using fermentation for additional ATP (which is inefficient).

Role of Proteome Physical Chemistry in Cell Behavior.

We review how major cell behaviors, such as bacterial growth laws, are derived from the physical chemistry of the cell's proteins. On one hand, cell actions depend on the individual biological functionalities of their many genes and proteins. On the other hand, the common physics among proteins can be as important as the unique biology that distinguishes them.

Highly Charged Proteins: The Achilles' Heel of Aging Proteomes.

As cells and organisms age, their proteins sustain increasing amounts of oxidative damage. It is estimated that half of all proteins are damaged in old organisms, yet the dominant mechanisms by which damage affects proteins and cellular phenotypes are not known. Here, we show that random modification of side chain charge induced by oxidative damage is likely to be a dominant source of protein stability loss in aging cells.

DNA Bending through Large Angles Is Aided by Ionic Screening.

We used adaptive umbrella sampling on a modified version of the roll angle to simulate the bending of DNA dodecamers. Simulations were carried out with the AMBER and CHARMM force fields for 10 sequences in which the central base pair step was varied. On long length scales, the DNA behavior was found to be consistent with the worm-like chain model.

Protein unfolding under force: crack propagation in a network.

The mechanical unfolding of a set of 12 proteins with diverse topologies is investigated using an all-atom constraint-based model. Proteins are represented as polypeptides cross-linked by hydrogen bonds, salt bridges, and hydrophobic contacts, each modeled as a harmonic inequality constraint capable of supporting a finite load before breaking. Stereochemically acceptable unfolding pathways are generated by minimally overloading the network in an iterative fashion, analogous to crack propagation in solids.

The long-wavelength limit of the structure factor of amorphous silicon and vitreous silica.

Liquids are in thermal equilibrium and have a non-zero structure factor S(Q --> 0) = [-(2)]/ = rho(0)k(B)Tchi(T) in the long-wavelength limit where rho(0) is the number density, T is the temperature, Q is the scattering vector and chi(T) is the isothermal compressibility. The first part of this result involving the number N (or density) fluctuations is a purely geometrical result and does not involve any assumptions about thermal equilibrium or ergodicity, so is obeyed by all materials. From a large computer model of amorphous silicon, local number fluctuations extrapolate to give S(0) = 0.

Hierarchical plasticity from pair distance fluctuations.

Observations, experiments and simulations often generate large numbers of snapshots of configurations of complex many-body systems. It is important to find methods of extracting useful information from these ensembles of snapshots in order to document the motion as the system evolves in time. Some of the most interesting information is contained in the relative motion of individual constituents, rather than their absolute motion.