Analysis of root-environment interactions reveals mechanical advantages of growth-driven penetration of roots.

Plant roots are considered highly efficient soil explorers. As opposed to the push-driven penetration strategy commonly used by many digging organisms, roots penetrate by growing, adding new cells at the tip, and elongating over a well-defined growth zone. However, a comprehensive understanding of the mechanical aspects associated with root penetration is currently lacking.

Strain Gradient Programming in 3D Fibrous Hydrogels to Direct Graded Cell Alignment.

Biological tissues experience various stretch gradients which act as mechanical signaling from the extracellular environment to cells. These mechanical stimuli are sensed by cells, triggering essential signaling cascades regulating cell migration, differentiation, and tissue remodeling. In most previous studies, a simple, uniform stretch to 2D elastic substrates has been applied to analyze the response of living cells.

Does the Extracellular Matrix Support Cell-Cell Communication by Elastic Wave Packets?

The extracellular matrix (ECM) is a fibrous network supporting biological cells and provides them a medium for interaction. Cells modify the ECM by applying traction forces, and these forces can propagate to long ranges and establish a mechanism of mechanical communication between neighboring cells. Previous studies have mainly focused on analysis of static force transmission across the ECM.

FITC-Dextran Release from Cell-Embedded Fibrin Hydrogels.

Fibrin hydrogel is a central biological material in tissue engineering and drug delivery applications. As such, fibrin is typically combined with cells and biomolecules targeted to the regenerated tissue. Previous studies have analyzed the release of different molecules from fibrin hydrogels; however, the effect of embedded cells on the release profile has yet to be quantitatively explored.

Controlled Strain of 3D Hydrogels under Live Microscopy Imaging.

External forces are an important factor in tissue formation, development, and maintenance. The effects of these forces are often studied using specialized in vitro stretching methods. Various available systems use 2D substrate-based stretchers, while the accessibility of 3D techniques to strain soft hydrogels, is more restricted.

Motion magnification analysis of microscopy videos of biological cells.

It is well recognized that isolated cardiac muscle cells beat in a periodic manner. Recently, evidence indicates that other, non-muscle cells, also perform periodic motions that are either imperceptible under conventional lab microscope lens or practically not easily amenable for analysis of oscillation amplitude, frequency, phase of movement and its direction. Here, we create a real-time video analysis tool to visually magnify and explore sub-micron rhythmic movements performed by biological cells and the induced movements in their surroundings.

Straining 3D Hydrogels with Uniform Z-Axis Strains While Enabling Live Microscopy Imaging.

External forces play an important role in the development and regulation of many tissues. Such effects are often studied using specialized stretchers-standardized commercial and novel laboratory-designed. While designs for 2D stretchers are abundant, the range of available 3D stretcher designs is more limited, especially when live imaging is required.

Force chains in cell-cell mechanical communication.

Force chains (FCs) are a key determinant of the micromechanical properties and behaviour of heterogeneous materials, such as granular systems. However, less is known about FCs in fibrous materials, such as the networks composing the extracellular matrix (ECM) of biological systems. Using a finite-element computational model, we simulated the contraction of a single cell and two nearby cells embedded in two-dimensional fibrous elastic networks and analysed the tensile FCs that developed in the ECM.

Local Ordering at Mobile Sites in Proteins: Combining Perspectives from NMR Relaxation and Molecular Dynamics.

We report on progress toward improving NMR relaxation analysis in proteins in terms of the slowly relaxing local structure (SRLS) approach by developing a method that combines SRLS with molecular dynamics (MD) simulations. N-H bonds from the Rho GTPase binding domain of plexin-B1 are used as test case. We focus on the locally restricting/ordering potential of mean force (POMF), u(θ,φ), at the N-H site (θ and φ specify the orientation of the N-H bond in the protein).

Nonlinear Elasticity of the ECM Fibers Facilitates Efficient Intercellular Communication.

Biological cells embedded in fibrous matrices have been observed to form intercellular 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. This 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.

Conformational Entropy from NMR Relaxation in Proteins: The SRLS Perspective.

Conformational entropy changes associated with bond-vector motions in proteins contribute to the free energy of ligand-binding. To derive such contributions, we apply the slowly relaxing local structure (SRLS) approach to NMR relaxation from N-H bonds or C-CDH moieties of several proteins in free and ligand-bound form. The spatial restraints on probe motion, which determine the extent of local order, are expressed in SRLS by a well-defined potential, u(θ).

An SRLS Study of H Methyl-Moiety Relaxation and Related Conformational Entropy in Free and Peptide-Bound PLC1C SH2.

The two-body (protein and probe) coupled-rotator slowly relaxing local structure (SRLS) approach for NMR relaxation in proteins is extended to derive conformational entropy, Ŝ. This version of SRLS is applied to deuterium relaxation from the C-CDH bonds of free and peptide-bound PLC1C SH2. Local C-CDH motion is described by a correlation time for local diffusion, τ, and a Maier-Saupe potential, u.

Local Ordering at Mobile Sites in Proteins from Nuclear Magnetic Resonance Relaxation: The Role of Site Symmetry.

Restricted motions in proteins (e.g., N-H bond dynamics) are studied effectively with NMR.

Polar Versus Non-polar Local Ordering at Mobile Sites in Proteins: Slowly Relaxing Local Structure Analysis of (15)N Relaxation in the Third Immunoglobulin-Binding Domain of Streptococcal Protein G.

We developed recently the slowly relaxing local structure (SRLS) approach for studying restricted motions in proteins by NMR. The spatial restrictions have been described by potentials comprising the traditional L = 2, K = 0, 2 spherical harmonics. However, the latter are associated with non-polar ordering whereas protein-anchored probes experience polar ordering, described by odd-L spherical harmonics.

Structural Dynamics of the Potassium Channel Blocker ShK: SRLS Analysis of (15)N Relaxation.

The 35-residue ShK peptide binds with high affinity to voltage-gated potassium channels. The dynamics of the binding surface was studied recently with (microsecond to millisecond) (15)N relaxation dispersion and (picosecond to nanosecond) (15)N spin relaxation of the N-H bonds. Relaxation dispersion revealed microsecond conformational-exchange-mediated exposure of the functionally important Y23 side chain to the peptide surface.

An extended CCR5 ECL2 peptide forms a helix that binds HIV-1 gp120 through non-specific hydrophobic interactions.

Unlabelled: C-C chemokine receptor 5 (CCR5) serves as a co-receptor for HIV-1. The CCR5 N-terminal segment, the second extracellular loop (ECL2) and the transmembrane helices have been implicated in binding the envelope glycoprotein gp120. Peptides corresponding to the sequence of the putative ECL2 as well as peptides containing extracellular loops 1 and 3 (ECL1 and ECL3) were found to inhibit HIV-1 infection.

Drosophila Raf's N terminus contains a novel conserved region and can contribute to torso RTK signaling.

Drosophila Raf (DRaf) contains an extended N terminus, in addition to three conserved regions (CR1-CR3); however, the function(s) of this N-terminal segment remains elusive. In this article, a novel region within Draf's N terminus that is conserved in BRaf proteins of vertebrates was identified and termed conserved region N-terminal (CRN). We show that the N-terminal segment can play a positive role(s) in the Torso receptor tyrosine kinase pathway in vivo, and its contribution to signaling appears to be dependent on the activity of Torso receptor, suggesting this N-terminal segment can function in signal transmission.

Regulation of energy liberation during steady sarcomere shortening.

Energy liberation rate (E) during steady muscle shortening is a monotonic increasing or biphasic function of the shortening velocity (V). The study examines three plausible hypotheses for explaining the biphasic E-V relationship (EVR): 1) the cross-bridge (XB) turnover rate from non-force-generating (weak) to force-generating (strong) conformation decreases as V increases; 2) XB kinetics is determined by the number of strong XBs (XB-XB cooperativity); and 3) the affinity of troponin for calcium is modulated by the number of strong XBs (XB-Ca cooperativity). The relative role of the various energy-regulating mechanisms is not well defined.

Is peptide bond cis/trans isomerization a key stage in the chemo-mechanical cycle of motor proteins?

Motor proteins such as myosin and kinesin are responsible for actively directed movement in vivo. The physicochemical mechanism underlying their function is still obscure. A novel and unifying model concerning the motors driving mechanism is suggested here.