BJ Articles Ahead of Print

We use optical tweezers microrheology and fluorescence microscopy to characterize the nonlinear mesoscale mechanics and mobility of in vitro co-entangled actin-microtubule composites. We create a suite of randomly-oriented, well-mixed networks of actin and microtubules by co-polymerizing varying ratios of actin and tubulin in situ. To perturb each composite far from equilibrium, we use optical tweezers to displace an embedded microsphere a distance greater than the lengths of the filaments at a speed much faster than their intrinsic relaxation rates.

A synergistic enhancement of activities has been described for the amphipathic cationic antimicrobial peptides magainin 2 and PGLa when tested in antimicrobial assays or in biophysical experiments using model membranes. In the presence of magainin 2, PGLa changes from an in-planar alignment parallel to the membrane surface to a more transmembrane orientation when investigated in membranes made from fully saturated PC or PC/PG, but not when one of the fatty acyl chains is unsaturated. Such lipid-mediated changes in the membrane topology of polypeptide domains could provide an interesting mechanism for the regulation of membrane proteins.

The copper-transporting ATPase ATP7B is essential for loading of copper ions to copper-dependent enzymes in the secretory pathway; its inactivation results in Wilson disease. In contrast to copper ion uptake by the cytoplasmic domains, ATP7B-mediated copper ion release in the Golgi has not been explored yet. We here demonstrate that a luminal loop in ATP7B, rich in histidine/methionine residues, binds reduced copper (Cu(I)) ions and identified copper-binding residues play an essential role in ATP7B-mediated metal ion release.

Given its ability to measure multicomponent distance distributions between electron-spin probes, Double Electron-Electron Resonance spectroscopy (DEER) has become a leading technique to assess the structural dynamics of biomolecules. However, methodologies to evaluate the statistical error of these distributions are not standard, often hampering a rigorous interpretation of the experimental results. Distance distributions are often determined from the experimental DEER data through a mathematical method known as Tikhonov regularization, but this approach makes rigorous error estimates difficult.

We examine the adhesion of biomembranes to substrates topographically patterned with concave nanopits, and identify several universal features in the adhesion process. We find three distinct states, depending on whether the membrane remains flat above the nanopit, partially enters it, or completely adheres to it, and derive analytical conditions for the stability of these states valid for a very general class of nanopit shapes. Surprisingly, completely adhered states are always (meta)stable. We also show that the presence of many nanopits can increase or decrease the effective adhesiveness of a substrate, depending on the tension of the membrane and the strength of the membrane–substrate attraction.

Recently, it has been reported that the cells of the immune system, as well as dictyostelium amoebae, can swim in a bulk fluid by changing their shape repeatedly. We refer to this motion as the amoeboid swimming. Here, we explore how the propulsion and the deformation of the cell emerges as an interplay between the active forces that the cell employs to activate the shape changes, and the passive, visco–elastic response of the cell membrane, the cytoskeleton, and the surrounding environment. We introduce a model, in which the cell is represented by an elastic capsule enclosing a viscous liquid.

Interactions between emerging nascent polypeptide chains and the ribosome can affect cotranslational protein folding. However, it has remained unclear how such interactions can affect the binding of nascent chains to their cellular targets. We thus investigated, on the ribosome, the interaction between the two intrinsically disordered proteins of opposite charge, ACTR and NCBD, which form a high-affinity complex in a coupled folding-and-binding reaction. Using fluorescence correlation spectroscopy and arrest-peptide-mediated force measurements in vitro and in vivo, we find that the ACTR-NCBD complex can form cotranslationally, but only with ACTR as the nascent chain and NCBD free in solution, not vice versa.

Biological cells embedded in fibrous matrices have been observed to form inter-cellular bands of dense and aligned fibers, through which they mechanically interact over long distances. Such matrix-mediated cellular interactions have been shown to regulate various biological processes. The current study aimed to explore the effects of elastic nonlinearity of the fibers contained in the extracellular matrix (ECM) on the transmission of mechanical loads between contracting cells. Based on our biological experiments, we developed a finite-element model of two contracting cells embedded within a fibrous network.

Long QT syndrome type 2 (LQT2) is a congenital disease characterized by loss of function mutations in hERG potassium channels (IKr). LQT2 is associated with fatal ventricular arrhythmias promoted by triggered activity in the form of early afterdepolarizations (EADs). We previously demonstrated that intracellular Ca2+ handling is remodeled in LQT2 myocytes. Remodeling leads to aberrant late RyR-mediated Ca2+ releases that drive forward-mode Na+-Ca2+ exchanger (NCX) current and slow repolarization to promote reopening of L-type calcium channels and EADs.

Conformational fluctuations of proteins are crucially important for their functions. However, changes in the location and dynamics of hydrated water in many proteins accompanied by the conformational transition have not been fully understood. Here, we used phase-modulated clean chemical exchange (CLEANEX-PM) NMR approach to investigate pressure-induced changes in water-to-amide proton exchange occurring at sub-second time scale. With the transition of ubiquitin from its native conformation (N1) to an alternative conformation (N2) at 250 MPa, proton exchange rates of residues 32–35, 40–41, and 71, which are located at the C-terminal side of the protein, were significantly increased.

With almost no consensus promoter sequence in prokaryotes, recruitment of RNA polymerase (RNAP) to precise transcriptional start sites (TSSs) has remained an unsolved puzzle. Uncovering the underlying mechanism is critical for understanding the principle of gene regulation. We attempted to search the hidden code in ∼16500 promoters, of twelve prokaryotes representing two kingdoms, in their structure and energetics. Twenty eight fundamental parameters of DNA structure including backbone angles, base pair axis, inter base pair and intra base pair parameters were used and information was extracted from X-ray crystallography (XRC) data.

The energy function is the key component of protein modeling methodology. The paper presents a semi-analytical approach to the development of contact potentials for protein structure modeling. Residue-residue and atom-atom contact energies were derived by maximizing the probability of observing native sequences in a non-redundant set of protein structures. The optimization task was formulated as an inverse statistical mechanics problem applied to the Potts model. Its solution by pseudo-likelihood maximization provides consistent estimates of coupling constants at atomic and residue levels.