Molecular Basis of the Mechanical Hierarchy in Myomesin Dimers for Sarcomere Integrity

Myomesin is one of the most important structural molecules constructing the M-band in the force-generating unit of striated muscle, and a critical structural maintainer of the sarcomere. Using molecular dynamics simulations, we here dissect the mechanical properties of the structurally known building blocks of myomesin, namely α-helices, immunglobulin (Ig) domains, and the dimer interface at myomesin’s 13th Ig domain, covering the mechanically important C-terminal part of the molecule. We find the interdomain α-helices to be stabilized by the hydrophobic interface formed between the N-terminal half of these helices and adjacent Ig domains, and, interestingly, to show a rapid unfolding and refolding equilibrium especially under low axial forces up to ∼15 pN. These results support and yield atomic details for the notion of recent atomic-force microscopy experiments, namely, that the unique helices inserted between Ig domains in myomesin function as elastomers and force buffers. Our results also explain how the C-terminal dimer of two myomesin molecules is mechanically outperforming the helices and Ig domains in myomesin and elsewhere, explaining former experimental findings. This study provides a fresh view onto how myomesin integrates elastic helices, rigid immunoglobulin domains, and an extraordinarily resistant dimer into a molecular structure, to feature a mechanical hierarchy that represents a firm and yet extensible molecular anchor to guard the stability of the sarcomere.     

On the Molecular Basis for Mechanotransduction

Much is currently known about the signaling pathways that are excited when cells are subjected to a mechanical stimulus, yet we understand little of the process by which the mechanical perturbation is transformed into a biochemical signal. Numerous theories have been proposed, and each has merit. While cells may possess many different ways of responding to stress, the existence of a single unifying principle has much appeal. Here we propose the hypothesis that cells sense mechanical force through changes in protein conformation, leading to altered binding affinities of proteins, ultimately initiating an intracellular signaling cascade or producing changes in the proteins localized to regions of high stress. More generally, this represents an alternative to transmembrane signaling through receptor-ligand interactions providing the cell with a means of reacting to changes in its mechanical, as opposed to biochemical, environment. One example is presented showing how the binding affinity between the focal adhesion targeting domain of focal adhesion kinase and the LD motif of paxillin is influenced by externally applied force.     

The Structural Basis for the Integrity of Adenovirus Ad3 Dodecahedron

During the viral life cycle adenoviruses produce excess capsid proteins. Human adenovirus serotype 3 (Ad3) synthesizes predominantly an excess of free pentons, the complexes of pentameric penton base and trimeric fiber proteins, which are responsible for virus penetration. In infected cells Ad3 pentons spontaneously assemble into dodecahedral virus-like nano-particles containing twelve pentons. They also form in insect cells during expression in the baculovirus system. Similarly, in the absence of fiber protein dodecahedric particles built of 12 penton base pentamers can be produced. Both kinds of dodecahedra show remarkable efficiency of intracellular penetration and can be engineered to deliver several millions of foreign cargo molecules to a single target cell. For this reason, they are of great interest as a delivery vector. In order to successfully manipulate this potential vector for drug and/or gene delivery, an understanding of the molecular basis of vector assembly and integrity is critical. Crystallographic data in conjunction with site-directed mutagenesis and biochemical analysis provide a model for the molecular determinants of dodecamer particle assembly and the requirements for stability. The 3.8 Å crystal structure of Ad3 penton base dodecamer (Dd) shows that the dodecahedric structure is stabilized by strand-swapping between neighboring penton base molecules. Such N-terminal strand-swapping does not occur for Dd of Ad2, a serotype which does not form Dd under physiological conditions. This unique stabilization of the Ad3 dodecamer is controlled by residues 59–61 located at the site of strand switching, the residues involved in putative salt bridges between pentamers and by the disordered N-terminus (residues 1–47), as confirmed by site directed mutagenesis and biochemical analysis of mutant and wild type protein. We also provide evidence that the distal N-terminal residues are externally exposed and available for attaching cargo.     

Col11a2 Deletion Reveals the Molecular Basis for Tectorial Membrane Mechanical Anisotropy

The tectorial membrane (TM) has a significantly larger stiffness in the radial direction than other directions, a prominent mechanical anisotropy that is believed to be critical for the proper functioning of the cochlea. To determine the molecular basis of this anisotropy, we measured material properties of TMs from mice with a targeted deletion of Col11a2, which encodes for collagen XI. In light micrographs, the density of TM radial collagen fibers was lower in Col11a2 -/- mice than wild-types. Tone-evoked distortion product otoacoustic emission and auditory brainstem response measurements in Col11a2 -/- mice were reduced by 30-50 dB independent of frequency as compared with wild-types, showing that the sensitivity loss is cochlear in origin. Stress-strain measurements made using osmotic pressure revealed no significant dependence of TM bulk compressibility on the presence of collagen XI. Charge measurements made by placing the TM as an electrical conduit between two baths revealed no change in the density of charge affixed to the TM matrix in Col11a2 -/- mice. Measurements of mechanical shear impedance revealed a 5.5 ± 0.8 dB decrease in radial shear impedance and a 3.3 ± 0.3 dB decrease in longitudinal shear impedance resulting from the Col11a2 deletion. The ratio of radial to longitudinal shear impedance fell from 1.8 ± 0.7 for TMs from wild-type mice to 1.0 ± 0.1 for those from Col11a2 -/- mice. These results show that the organization of collagen into radial fibrils is responsible for the mechanical anisotropy of the TM. This anisotropy can be attributed to increased mechanical coupling provided by the collagen fibrils. Mechanisms by which changes in TM material properties may contribute to the threshold elevation in Col11a2 -/- mice are discussed.     

Mechanical Properties of the Sarcolemma and Myoplasm in Frog Muscle as a Function of Sarcomere Length

The elastimeter method was applied to the single muscle fiber of the frog semitendinosus to obtain the elastic moduli of the sarcolemma and myoplasm, as well as their relative contributions to resting fiber tension at different extensions. A bleb which was sucked into a flat-mouthed pipette at the fiber surface separated into an external sarcolemmal membrane and a thick inner myoplasmic region. Measurements showed that the sarcolemma does not contribute to intact fiber tension at sarcomere lengths below 3 µ. It was estimated that the sarcolemma contributed on the order of 10% to intact fiber tension at sarcomere lengths between 3 and 3.75 µ, and more so with further extension. Between these sarcomere lengths, the sarcolemma can be linearly extended and has a longitudinal elastic modulus of 5 x 10⁶ dyne/cm² (assuming a thickness of 0.1 µ). Resistance to deformation of the inner bleb region is due to myoplasmic elasticity. The myoplasmic elastic modulus was estimated by use of a model and was used to predict a fiber length-tension curve which agreed approximately with observations.     

Molecular Basis for Fibrillar Aggregation of Tropocollagen

NO model for the three dimensional packing of tropocollagen (TC) molecules into fibrils^1–3 approaches the problem on a molecular level; such analysis requires the assumption of a specific macromolecular structure^4–6 and of a specific aggregation state^7,8 of TC molecules. If the Ramachandran, Rich and Crick structure with the a1 chains in register from the N-terminus and the quarter stagger mode of association are assumed, then corresponding residues in the a chains will be separated by 108° radial angles^4,6. Possible intermolecular associations, producing quarter-staggered⁷ TC aggregation, fall into two general classes: (1) association involving a single chain in one molecule with a single chain in another and (2) complex association loci involving more than one chain in each TC molecule. The former is the more likely possibility and would involve residues on an individual a chain, at intervals governed by the pitch of the super helix, forming a longitudinal edge which associates in a defined plane of contact with a complementary edge in a neighbouring TC molecule^2,4,6.     

Molecular Basis for the Transformation Defects in Mutants of Haemophilus influenzae

To determine the molecular basis of transformation defects in Haemophilus influenzae, the fate of genetically marked, (32)P-labeled, heavy deoxyribonucleic acid (DNA) was examined in three mutant strains (rec(1) (-), rec(2) (-), and KB6) and in wild type having (3)H-labeled DNA and a second genetic marker. Transforming cells upon lysis with digitonin followed by low-speed centrifugation are separable into the supernatant fraction, containing mainly the unintegrated donor DNA, and the pellet, containing most of the resident DNA along with integrated donor DNA. Electron micrographs of digitonin-treated cells also indicate that the resident DNA is trapped inside a cellular structure but that cytoplasmic elements such as ribosomes are extensively released. DNA synthesis in digitonin-treated cells is immediately blocked, as is any further integration of donor DNA into the resident genome. Isopycnic and sedimentation analysis of supernatant fluids and pellets revealed that in strains rec(2) (-) and KB6 there is little or no association between donor and resident DNA, and thus there is negligible transfer of donor DNA genetic information. In these strains, the donor DNA is not broken into pieces of lower molecular weight as it is in strain rec(1) (-) and in the wild type, both of which show association between donor and recipient DNA. In strain rec(1) (-), although some donor DNA atoms become covalently linked to resident DNA, the incorporated material does not have the donor DNA transforming activity.     

小鼠胚胎紧密化现象分子基础的研究进展

就小鼠植入前胚胎紧密化过程中胚胎的形态变化、细胞极化、细胞间连接及紧密化的物质基础、时控机制等作了综述.对紧密化现象的分子基础研究大多数都集中在翻译后水平的调控,而在基因水平的研究较少.     

Dimers and Trimers of Chondroitin in Molecular Docking of Bovine Testicular Hyaluronidase

Russian Journal of Bioorganic Chemistry - Molecular docking of a 3D model of bovine testicular hyaluronidase was performed with dimers and trimers of chondroitin. On the molecular surface of a...     

A Molecular Structural Basis for the Excitation Properties of Axons

A structural model is suggested for axon membranes consisting of a double layer of lipid and phospholipid molecules in which the polar ends of certain phospholipids change their orientation and combining properties under the influence of an electric field. The phosphate groups act as ion exchange “gates” for the control of ion flow through the membrane. Expressions are developed for the calculation of membrane current components as functions of time, potential, and ionic environment. Approximate solutions show fairly good agreement with existing experimental data in a number of different respects such as steady-state current-voltage relations, the effect of calcium on steady-state current, potassium tracer flux ratios, initial current and rate of change of current, and the dependence of the time constants of current change on membrane potential.     

Molecular Basis for the Single-Nucleotide Precision of Primary microRNA Processing

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Molecular Basis for the Inhibition of p53 by Mdmx

The oncoprotein Mdm2, and the recently intensely studied, homologues protein Mdmx, are principal negative regulators of the p53 tumor uppressor. The mechanisms by which they regulate the stability and activity of p53 are not fully established. We have determined the crystal structure of the N-terminal domain of Mdmx bound to a 15-residue p53 peptide. The structure reveals that although the principle features of the Mdm2-p53 interaction are preserved in the Mdmx-p53 complex, the Mdmx hydrophobic cleft on which the p53 peptide binds is significantly altered: a part of the cleft is blocked by sidechains of Met and Tyr of the p53-binding pocket of Mdmx. Thus specific inhibitors of Mdm2-p53 would not be optimal for binding to Mdmx. Our binding assays show indeed that nutlins, the newly discovered, potent antagonists of the Mdm2-p53 interaction, are notcapable to efficiently disrupt the Mdmx-p53 interaction. To achieve full activation of p53 in tumor cells, compounds that are specific for Mdmx are necessary to complement the Mdm2 specific binders.     

Structural Basis for Elastic Mechanical Properties of the DNA Double Helix

In this article, we investigate the principal structural features of the DNA double helix and their effects on its elastic mechanical properties. We develop, in the pursuit of this purpose, a helical continuum model consisting of a soft helical core and two stiff ribbons wrapping around it. The proposed model can reproduce the negative twist-stretch coupling of the helix successfully as well as its global stretching, bending, and torsional rigidities measured experimentally. Our parametric study of the model using the finite element method further reveals that the stiffness of phosphate backbones is a crucial factor for the counterintuitive overwinding behavior of the duplex and its extraordinarily high torsional rigidity, the major-minor grooves augment the twist-stretch coupling, and the change of the helicity might be responsible for the transition from a negative to a positive twist-stretching coupling when a tensile force is applied to the duplex.