Microtubules are hollow cylindrical structures that constitute one of the three major classes of cytoskeletal filaments. On the mesoscopic length scale of a cell, their material properties are characterized by a single stiffness parameter, the persistence length ഞp. Its value, in general, depends on the microscopic interactions between the constituent tubulin dimers and the architecture of the microtubule. Here, we use single-particle tracking methods combined with a fluctuation analysis to systematically study the dependence of ഞ p on the total filament length L. Microtubules are grafted to a substrate with one end free to fluctuate in three dimensions. A fluorescent bead is attached proximally to the free tip and is used to record the thermal fluctuations of the microtubule's end. The position distribution functions obtained with this assay allow the precise measurement of ഞ p for microtubules of different contour length L. Upon varying L between 2.6 and 47.5 m, we find a systematic increase of ഞp from 110 to 5,035 m. At the same time we verify that, for a given filament length, the persistence length is constant over the filament within the experimental accuracy. We interpret this length dependence as a consequence of a nonnegligible shear deflection determined by subnanometer relative displacement of adjacent protofilaments. Our results may shine new light on the function of microtubules as sophisticated nanometer-sized molecular machines and give a unified explanation of seemingly uncorrelated spreading of microtubules' stiffness previously reported in literature.nanomechanics ͉ protofilaments ͉ single-particle tracking ͉ thermal fluctuation analysis T he mechanics of living cells is largely determined by the cytoskeleton, a self-organizing and highly dynamic network of filamentous proteins of different lengths and stiffnesses (1). Understanding the elastic response of purified cytoskeletal filaments is fundamental for the elucidation of the rheological behavior of the cytoskeleton. Microtubules (MTs) are hollow cylindrical filaments formed by, on average, 13 tubulin protofilaments (PFs) assembled in parallel. The MT outer and inner diameters are Ϸ25 and 15 nm, respectively. In cells, MTs are generally 1-10 m long, whereas in axons their length can be 50-100 m (2).The tubular structure of MTs implies a minimal crosssectional area, hence a high strength and stiffness combined with low density. In recent years, the mechanical properties of MTs have been investigated by several experimental approaches, such as thermal fluctuations (3-6), atomic force microscopy (AFM) (7-10), and optical tweezers (11-13).The standard reference model to describe the mechanical properties of a biopolymer on length scales much larger than any microscopic scale (the tube diameter for MTs) is the worm-like chain model (14,15). It is characterized in terms of a flexural rigidity (neglecting torsional rigidity). The combined effect of flexural rigidity and thermal fluctuations on the conformation of the filament is given by the ratio ...

Peripheral events in olfaction involve odorant binding proteins (OBPs) whose role in the recognition of different volatile chemicals is yet unclear. Here we report on the sensitive and quantitative measurement of the weak interactions associated with neutral enantiomers differentially binding to OBPs immobilized through a self-assembled monolayer to the gate of an organic bio-electronic transistor. The transduction is remarkably sensitive as the transistor output current is governed by the small capacitance of the protein layer undergoing minute changes as the ligand–protein complex is formed. Accurate determination of the free-energy balances and of the capacitance changes associated with the binding process allows derivation of the free-energy components as well as of the occurrence of conformational events associated with OBP ligand binding. Capacitance-modulated transistors open a new pathway for the study of ultra-weak molecular interactions in surface-bound protein–ligand complexes through an approach that combines bio-chemical and electronic thermodynamic parameters.

Aquaporin-4 (AQP4) is the predominant water channel in different organs and tissues. An alteration of its physiological functioning is responsible for several disorders of water regulation and, thus, is considered an attractive target with a promising therapeutic and diagnostic potential. Molecular dynamics (MD) simulations performed on the AQP4 tetramer embedded in a bilayer of lipid molecules allowed us to analyze the role of spontaneous fluctuations occurring inside the pore. Following the approach by Hashido et al. [Hashido M, Kidera A, Ikeguchi M (2007) Biophys J 93: 373-385], our analysis on 200ns trajectory discloses three domains inside the pore as key elements for water permeation. Herein, we describe the gating mechanism associated with the well-known selectivity filter on the extracellular side of the pore and the crucial regulation ensured by the NPA motifs (asparagine, proline, alanine). Notably, on the cytoplasmic side, we find a putative gate formed by two residues, namely, a cysteine belonging to the loop D (C178) and a histidine from loop B (H95). We observed that the spontaneous reorientation of the imidazole ring of H95 acts as a molecular switch enabling H-bond interaction with C178. The occurrence of such local interaction seems to be responsible for the narrowing of the pore and thus of a remarkable decrease in water flux rate. Our results are in agreement with recent experimental observations and may represent a promising starting point to pave the way for the discovery of chemical modulators of AQP4 water permeability.

Nanoscale and microscale confinement of biopolymers naturally occurs in cells and has been recently achieved in artificial structures designed for nanotechnological applications. Here, we present an extensive theoretical investigation of the conformations and shape of a biopolymer with varying stiffness confined to a narrow channel. Combining scaling arguments, analytical calculations, and Monte Carlo simulations, we identify various scaling regimes where master curves quantify the functional dependence of the polymer conformations on the chain stiffness and strength of confinement. DOI: 10.1103/PhysRevE.75.050902 PACS number͑s͒: 87.16.Ac, 36.20.Ey, 82.35.Lr, 87.16.Ka What is the effect of confinement on the shape of a biopolymer? With recent advances in visualizing and manipulating macromolecules on ever shrinking length scales, an answer to this question has gained increasing importance. In the crowded environment of a cell the conformations of cytoskeletal filaments are highly constrained by other neighboring macromolecules. This confinement largely alters the viscoelastic response of entangled biopolymer solutions ͓1,2͔. There is growing interest in manufacturing nanostructures such as nanopores ͓3͔ and nanochannels ͓4,5͔ for investigating and manipulating DNA with improved technologies aiming toward smaller and smaller structures. Hence an improved understanding of the effect of confinement on biopolymer conformations has potential implications for the design of nanoscale devices in biotechnological applications. Similarly, microfluidic devices have been used to explore confinement effects on actin filaments and DNA ͓6,7͔. What makes the confinement of biopolymers both a challenging and interesting problem is that biopolymers, unlike their synthetic counterparts, are generally stiff on a length scale much larger than their monomer size. The persistence length ᐉ p , the scale below which bending energy dominates over thermal fluctuations, is approximately 50 nm for DNA ͓8͔ and 16 m for F-actin ͓9͔. Depending on whether the contour length L is smaller or larger than the persistence length we may distinguish between stiff and flexible chains.For cellular systems as well as for nanoscale devices, biopolymers are confined on length scales comparable with their persistence length ᐉ p such that the polymer's intrinsic bending stiffness plays a decisive role for its conformations. For simplicity, consider a cylindrical tube of diameter d. Upon balancing the bending stiffness of a chain with thermal energy, Odijk ͓10͔ has identified a length L d measuring the typical distance between successive deflections of the chain, Fig. 1. This suggests to use the number of collisions c = L / L d per filament length L as a natural dimensionless parameter to measure the strength of confinement and = L / ᐉ p to measure the flexibility of a polymer. The physics in the strong confinement regime ͑c 1͒ is genuinely different from the regime where the radius of gyration R G of a long flexible chain ͑with L ᐉ p ͒ becomes comparable...

We explore the relation between the morphological and the charge transport properties of poly(3-hexylthiophene) (P3HT) and poly(2,5-bis(3-alkylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT) semiconductor polymers in both amorphous and crystalline phases. Using molecular dynamics to simulate bulk supercells and the Marcus theory to analyze the transport properties we found that amorphous systems display a reduced hole mobility due to the loss of nematic order and π-π stacking leading to a reduction in the electronic coupling between two chains. In the crystal phase, PBTTT displays a larger charge mobility than P3HT due to the interdigitation of the side chains enhancing the stability of the conjugated rings on the backbones. This more stable π-π stacking reduces the energetic disorder with respect to P3HT and increases the electronic coupling. In contrast, in the amorphous phase, PBTTT displays a reduced charge mobility with respect to P3HT due to the absence of side chains attached to the thienothiophenes, which increases their fluctuations and the energetic disorder. In addition, we show that it is possible to calculate the reorganization energy neglecting the side chains of the polymers and thus saving computational time. Within this approximation, we obtained mobility values matching the experimental measurements, thus confirming that the side chains are crucial to shape the morphology of the polymeric systems but are not involved in the charge transport process.