Viscous Friction of Hydrogen-Bonded Matter

Polymer physics view of peripheral chromatin: de Gennes' self-similar carpet

Using scaling arguments to model peripheral chromatin localized near the inner surface of the nuclear envelope (NE) as a flexible polymer chain, we discuss the structural properties of the peripheral chromatin composed of alternating lamin-associated domains (LADs) and inter-LADs. Modeling the attraction of LADs to NE by de Gennes' self-similar carpet, which treats the chromatin layer as a polymer fractal, explains two major experimental observations. (i) The high density of chromatin close to the nuclear periphery decays to a constant density as the distance to the periphery increases. (ii) Due to the decreasing mesh size towards the nuclear periphery, the chromatin carpet inside NE excludes molecules (via nonspecific interactions) above a threshold size that depends on the distance from the nuclear periphery.

Controlling Macroscopic Friction through Interfacial Siloxane Bonding

Controlling macroscopic friction is crucial for numerous natural and industrial applications, ranging from forecasting earthquakes to miniaturizing semiconductor devices, but predicting and manipulating friction phenomena remains a challenge due to the unknown relationship between nanoscale and macroscopic friction. Here, we show experimentally that dry friction at multiasperity Si-on-Si interfaces is dominated by the formation of interfacial siloxane (Si─O─Si) bonds, the density of which can be precisely regulated by exposing plasma-cleaned silicon surfaces to dry nitrogen. Our results show how the bond density can be used to quantitatively understand and control the macroscopic friction. Our findings establish a unique connection between the molecular scale at which adhesion occurs, and the friction coefficient that is the key macroscopic parameter for industrial and natural tribology challenges.

Local and Large-Scale Conformational Dynamics in Unfolded Proteins and IDPs. II. Effect of Temperature and Internal Friction

Internal dynamics of proteins are essential for protein folding and function. Dynamics in unfolded proteins are of particular interest since they are the basis for many cellular processes like folding, misfolding, aggregation, and amyloid formation and also determine the properties of intrinsically disordered proteins (IDPs). It is still an open question of what governs motions in unfolded proteins and whether they encounter major energy barriers. Here we use triplet-triplet energy transfer (TTET) in unfolded homopolypeptide chains and IDPs to characterize the barriers for local and long-range loop formation. The results show that the formation of short loops encounters major energy barriers with activation energies (Ea) up to 18 kJ/mol (corrected for effects of temperature on water viscosity) with very little dependence on amino acid sequence. For poly(Gly-Ser) and polySer chains the barrier decreases with increasing loop size and reaches a limiting value of 4.6 ± 0.4 kJ/mol for long and flexible chains. This observation is in accordance with the concept of internal friction encountered by chain motions due to steric effects, which is high for local motions and decreases with increasing loop size. Comparison with the results from the viscosity dependence of loop formation shows a negative correlation between Ea and the sensitivity of the reaction to solvent viscosity (α) in accordance with the Grote-Hynes theory of memory friction. The Arrhenius pre-exponential factor (A) also decreases with increasing loop size, indicating increased entropic costs for loop formation. Long-range loop formation in the investigated sequences derived from IDPs shows increased Ea and A compared with poly(Gly-Ser) and polySer chains. This increase is exclusively due to steric effects that cause additional internal friction, whereas intramolecular hydrogen bonds, dispersion forces, and charge interactions do not affect the activation parameters.

Effect of Charge State on the Equilibrium and Kinetic Properties of Mechanically Interlocked [5]Rotaxane: A Molecular Dynamics Study

Rotaxanes can exhibit stimuli-responsive behavior by allowing positional fluctuations of their rota groups in response to physiochemical conditions such as the changes in solution pH. However, ionic strength of the solution also affects the molecular conformation by altering the charge state of the entire molecule, coupling the stimuli-responsiveness of rotaxanes with their conformation. A molecular-scale investigation on a model system can allow the decoupling and identification of various effects and can greatly benefit applications of such molecular switches. By using atomistic molecular dynamics simulations, we study equilibrium and kinetics properties of various charge states of the [5]rotaxane, which is a supramolecular moiety with four rotaxanes bonded to a porphyrin core. We model various physiochemical charge states, each of which can be realized at various solution pH levels as well as several exotic charge distributions. By analyzing molecular configurations, hydrogen bonding, and energetics of single molecules in salt-free water and its polyrotaxanated network at the interface of water and chloroform, we demonstrate that charge-neutral and negatively charged molecules often tend to collapse in a way that they can expose their porphyrin core. Contrarily, positively charged moieties tend to take more extended molecular configurations blocking the core. Further, sudden changes in the charge states emulating the pH alterations in solution conditions lead to rapid, sub-10 ns level, changes in the molecular conformation of [5]rotaxane via shuttling motion of CB6 rings along axles. Finally, simulations of 2D [5]rotaxane network structures support our previous findings on a few nanometer-thick film formation at oil-water interfaces. Overall, our results suggest that rotaxane-based structures can exhibit a rich spectrum of molecular configurations and kinetics depending on the ionic strength of the solution.

Effects of interfacial dynamics on the damping of biocomposites

A damping model is developed based on the mechanism of interfacial interaction in nanoscale particle reinforced composites. The model includes the elasticity of the materials and the effects of interfacial adhesion hysteresis. Specific results are given for the case of bio-based PA610 polyamide reinforced by nanocrystalline cellulose (CNC), based on a previous study that showed this composite possesses very high damping. The presence of hydrogen bonding at the interface between the particle and matrix and the large interfacial area due to the filler's nano size are shown to be the main causes of the high damping enhancement. The influence of other parameters, such as interfacial distance and stiffness of the matrix materials are also discussed. The modeling work can be used as a guide in designing composites with good damping properties.

Ray Optics for Gliders

Control of self-propelled particles is central to the development of many microrobotic technologies, from dynamically reconfigurable materials to advanced lab-on-a-chip systems. However, there are few physical principles by which particle trajectories can be specified and can be used to generate a wide range of behaviors. Within the field of ray optics, a single principle for controlling the trajectory of light─Snell's law─yields an intuitive framework for engineering a broad range of devices, from microscopes to cameras and telescopes. Here we show that the motion of self-propelled particles gliding across a resistance discontinuity is governed by a variant of Snell's law, and develop a corresponding ray optics for gliders. Just as the ratio of refractive indexes sets the path of a light ray, the ratio of resistance coefficients is shown to determine the trajectories of gliders. The magnitude of refraction depends on the glider's shape, in particular its aspect ratio, which serves as an analogue to the wavelength of light. This enables the demixing of a polymorphic, many-shaped, beam of gliders into distinct monomorphic, single-shaped, beams through a friction prism. In turn, beams of monomorphic gliders can be focused by spherical and gradient friction lenses. Alternatively, the critical angle for total internal reflection can be used to create shape-selective glider traps. Overall our work suggests that furthering the analogy between light and microscopic gliders may be used for sorting, concentrating, and analyzing self-propelled particles.

Multivalent non-covalent interactions lead to strongest polymer adhesion

Multivalent interactions play a leading role in biological processes such as the inhibition of inflammation or virus internalization. The multivalent interactions show enhanced strength and better selectivity compared to monovalent interactions, but they are much less understood due to their complexity. Here, we detect molecular interactions in the range of a few piconewtons to several nanonewtons and correlate them with the formation and subsequent breaking of one or several bonds and assign these bonds. This becomes possible by performing atomic force microcopy (AFM)-based single molecule force spectroscopy of a multifunctional polymer covalently attached to an AFM cantilever tip on a substrate bound polymer layer of the multifunctional polymer. Varying the pH value and the crosslinking state of the polymer layer, we find that bonds of intermediate strength (non-covalent), like coordination bonds, give the highest multivalent bond strength, even outperforming strong (covalent) bonds. At the same time, covalent bonds enhance the polymer layer density, increasing in particular the number of non-covalent bonds. In summary, we can show that the key for the design of stable and durable polymer coatings is to provide a variety of multivalent interactions and to keep the number of non-covalent interactions at a high level.

Molecular origin of the effects of mutation on the structure and mechanical properties of human epithelial keratin K5/K14

Epithelial keratin, a type of intermediate filament (IF) protein, is one of the key components in maintaining the stability of the cell nucleus in the epidermis of the skin, the largest organ in the human body. It absorbs water and withstands external pressure, affecting the structural stability and mechanical properties of the skin. Epidermolysis bullosa simplex (EBS) is a rare genetic skin disease related to genetic mutations in epithelial keratin K5/K14. The resulting structural defects can cause keratinocytes in the basal layer to become fragile and rupture when subjected to mechanical stress. Its pathological feature is that the skin and mucous membranes are extremely fragile, and wounds and blisters occur under even slight external force. In this study, we focused on the amino acid sequence of the wild-type human keratin K5/K14 and sequences with point mutations, beginning with a full atomistic model of the K5/K14 heterodimer and proceeding to the higher hierarchical structure of the tetramer model. For the heterodimer, the structures of the wild type and the mutants share a high degree of similarity, and the helical structure is preserved. Then, based on the heterodimer model, we considered the keratin tetramer model with the ID1 contact from previous experimental observations. Our results suggested that in the wild-type tetramer, the hydrogen bonds formed in the middle and contact regions provide extra stability to tetramer 2B-2B interactions during IF assembly. The probabilities of hydrogen bond formation are lower in the mutant tetramers than in the wild-type tetramer in the contact region; the point mutations do not necessarily affect the structure for dimer formation, but changes in the interactions of amino acids may affect the higher-order assembly of IFs. We observed that the structures of the tetramers with point mutations were loosely stacked, and the mechanical properties were weaker than those of the wild-type tetramer. We further compared our results with the latest experimental measurements and discussed the relationship between the genotype of EBS disease and the atomic-level mutated structures. The atomistic model allowed us to study point mutations at the molecular level. The results can be further applied to reveal the effect of point mutations on EBS disease.

Origin of the Surprising Mechanical Stability of Kinesin's Neck Coiled Coil

Kinesin-1 is a motor protein moving along a microtubule with its two identical motor heads dimerized by two neck linkers and a coiled-coil stalk. When both motor heads bind the microtubule, an internal strain is built up between the two heads, which is indispensable to ensure proper coordination of the two motor heads during kinesin-1's mechanochemical cycle. The internal strain forms a tensile force along the neck linker that tends to unwind the neck coiled coil (NCC). Experiments showed that the kinesin-1's NCC has a high antiunwinding ability compared with conventional coiled coils, which was mainly attributed to the enhanced hydrophobic pressure arising from the unconventional sequence of kinesin-1's NCC. However, hydrophobic pressure cannot provide the shearing force which is needed to balance the tensile force on the interface between two helices. To find out the true origin of the mechanical stability of kinesin-1's NCC, we perform a novel and detailed mechanical analysis for the system based on molecular dynamics simulation at an atomic level. We find that the needed shearing force is provided by a buckle structure formed by two tyrosines which form effective steric hindrance in the presence of tensile forces. The tensile force is balanced by the tensile direction component of the contact force between the two tyrosines which forms the shearing force. The hydrophobic pressure balances the other component of the contact force perpendicular to the tensile direction. The antiunwinding strength of NCC is defined by the maximum shearing force, which is finally determined by the hydrophobic pressure. Kinesin-1 uses residues with plane side chains, tryptophans and tyrosines, to form the hydrophobic center and to shorten the interhelix distance so that a high antiunwinding strength is obtained. The special design of NCC ensures exquisite cooperation of steric hindrance and hydrophobic pressure that results in the surprising mechanical stability of NCC.

Unexpected large impact of small charges on surface frictions with similar wetting properties

Generally, the interface friction on solid surfaces is regarded as consistent with wetting behaviors, characterized by the contact angles. Here using molecular dynamics simulations, we find that even a small charge difference (≤0.36 e) causes a change in the friction coefficient of over an order of magnitude on two-dimensional material and lipid surfaces, despite similar contact angles. This large difference is confirmed by experimentally measuring interfacial friction of graphite and MoS₂ contacting on water, using atomic force microscopy. The large variation in the friction coefficient is attributed to the different fluctuations of localized potential energy under inhomogeneous charge distribution. Our results help to understand the dynamics of two-dimensional materials and biomolecules, generally formed by atoms with small charge, including nanomaterials, such as nitrogen-doped graphene, hydrogen-terminated graphene, or MoS₂, and molecular transport through cell membranes.

Organic Thermoelectric Multilayers with High Stretchiness

A stretchable organic thermoelectric multilayer is achieved by alternately depositing bilayers (BL) of 0.1 wt% polyethylene oxide (PEO) and 0.03 wt% double walled carbon nanotubes (DWNT), dispersed with 0.1 wt% polyacrylic acid (PAA), by the layer-by-layer assembly technique. A 25 BL thin film (~500 nm thick), composed of a PEO/DWNT-PAA sequence, displays electrical conductivity of 19.6 S/cm and a Seebeck coefficient of 60 µV/K, which results in a power factor of 7.1 µW/m·K2. The resultant nanocomposite exhibits a crack-free surface up to 30% strain and retains its thermoelectric performance, decreasing only 10% relative to the unstretched one. Even after 1000 cycles of bending and twisting, the thermoelectric behavior of this nanocomposite is stable. The synergistic combination of the elastomeric mechanical properties (originated from PEO/PAA systems) and thermoelectric behaviors (resulting from a three-dimensional conjugated network of DWNT) opens up the possibility of achieving various applications such as wearable electronics and sensors that require high mechanical compliance.

Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes

Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA that lead to the stability of the intercalated drug is lacking. Of particular interest are the modifications of the mechanical properties of dsDNA observed in experiments. The latter could affect many biological functions, such as DNA transcription and replication. Here, we probe, via all-atom molecular dynamics (MD) simulations, the change in the mechanical properties of intercalated drug-DNA complexes for two intercalators, daunomycin and ethidium. We find that, upon drug intercalation, the stretch modulus of DNA increases significantly, whereas its persistence length and bending modulus decrease. Steered MD simulations reveal that it requires higher forces to stretch the intercalated dsDNA complexes than the normal dsDNA. Adopting various pulling protocols to study force-induced DNA melting, we find that the dissociation of dsDNA becomes difficult in the presence of intercalators. The results obtained here provide a plausible mechanism of function of the anticancer drugs, i.e., via altering the mechanical properties of DNA. We also discuss long-time consequences of using these drugs, which require further in vivo investigations.

Nanoscale toughening of ultrathin graphene oxide-polymer composites: mechanochemical insights into hydrogen-bonding/van der Waals interactions, polymer chain alignment, and steric parameters

This paper describes a systematic study on the nanoscale toughening of monolayer graphene oxide (GO) by an ultra-thin polymer adlayer, which impedes the propagation of cracks during intraplanar fracture. Using molecular dynamics simulations, the crack-bridging capabilities of a library of five hydrogen-bonding-capable polymers are explored against an epoxide-rich GO substrate. The best crack-bridging effect is found in polymers with functional groups that can both donate/accept hydrogen atoms and have better capability to form cooperative hydrogen bonds. Aligning the chains of poly(acrylic acid) orthogonally to the crack propagation direction significantly enhances the fracture toughness of monolayer GO (by 310%) in comparison to that for an adlayer with randomly arranged chains (180% enhancement). Notably, van der Waals interactions, which are seldom highlighted in the fabrication of strong GO-polymer interfaces, are found to also provide significant crack-bridging capabilities when the polymers possess large side groups. These results pave the way for a set of design criteria that can help in remediating the intrinsically brittle mechanical behavior of two-dimensional materials, a barrier that currently restricts their potential applications.

Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics

We present an improved version of the ABSINTH implicit solvation model and force field paradigm (termed ABSINTH-C) by incorporating a grid-based term that bootstraps against experimentally derived and computationally optimized conformational statistics for blocked amino acids. These statistics provide high-resolution descriptions of the intrinsic backbone dihedral angle preferences for all 20 amino acids. The original ABSINTH model generates Ramachandran plots that are too shallow in terms of the basin structures and too permissive in terms of dihedral angle preferences. We bootstrap against the reference optimized landscapes and incorporate CMAP-like residue-specific terms that help us reproduce the intrinsic dihedral angle preferences of individual amino acids. These corrections that lead to ABSINTH-C are achieved by balancing the incorporation of the new residue-specific terms with the accuracies inherent to the original ABSINTH model. We demonstrate the robustness of ABSINTH-C through a series of examples to highlight the preservation of accuracies as well as examples that demonstrate the improvements. Our efforts show how the recent experimentally derived and computationally optimized coil-library landscapes can be used as a touchstone for quantifying errors and making improvements to molecular mechanics force fields.

Lubricating properties of single metal ions at interfaces

The behaviour of ionic solutions confined in nanoscale gaps is central to countless processes, from biomolecular function to electrochemistry, energy storage and lubrication. However, no clear link exists between the molecular-level behaviour of the liquid and macroscopic observations. The problem mainly comes from the difficulty to interrogate a small number of liquid molecules. Here, we use atomic force microscopy to investigate the viscoelastic behaviour of pure water and ionic solutions down to the single ion level. The results show a glassy-like behaviour for pure water, with single metal ions acting as lubricants by reducing the elasticity of the nano-confined solution and the magnitude of the hydrodynamic friction. At small ionic concentration (<20 mM) the results can be quantitatively explained by the ions moving via a thermally-activated process resisted by the ion's hydration water (Prandtl-Tomlinson model). The model breaks down at higher salt concentrations due to ion-ion interaction effects that can no longer be neglected. The correlations are confirmed by direct sub-nanometre imaging of the interface at equilibrium. The results provide a molecular-level basis for explaining the tribological properties of aqueous solutions and suggest that ion-ion interactions create mesoscale effects that prevent a direct link between nanoscale and macroscopic measurements.

The Influence of Hydroxyl Groups on Friction of Graphene at Atomic Scale

Hydroxyl groups play an important role in friction of graphene oxides. In this paper, the influence of hydroxyl groups on friction of graphene is investigated by molecular dynamics simulation. The results show that the friction does not always go up with the rising of hydroxyl groups ratio, and reaches the maximum when the hydroxyl groups ratio between interfaces is about 10%. The reason is that hydrogen bonds tend to form in interlayers when the hydroxyl groups ratio is high. The formed hydrogen bonds between interfaces are closely related to the friction. However, the analysis of the component of van der Waals, Coulomb’s forces and hydrogen bonds interaction between interfaces indicates that van der Waals forces are dominant in friction, which can be attributed to the influence of interface distance on friction.

Hydration Friction in Nanoconfinement: From Bulk via Interfacial to Dry Friction

The viscous properties of nanoscopically confined water are important when hydrated surfaces in close contact are sheared against each other. Numerous experiments have probed the friction between atomically flat hydrated surfaces in the subnanometer separation regime and suggested an increased water viscosity, but the value of the effective viscosity of ultraconfined water, the mechanism of hydration layer friction, and the crossover to the dry friction limit are unclear. We study the shear friction between polar surfaces by extensive nonequilibrium molecular dynamics simulations in the linear-response regime at low shearing velocity, which is the relevant regime for typical biological applications. With decreasing water film thickness we find three consecutive friction regimes: For thick films friction is governed by bulk water viscosity. At separations of about a nanometer the highly viscous interfacial water layers dominate and increase the surface friction, while at the transition to the dry friction limit interfacial slip sets in. Based on our simulation results, we construct a confinement-dependent friction model which accounts for the additive friction contributions from bulklike water, interfacial water layers, and interfacial slip and which is valid for arbitrary water film thickness.

Combined High Stretchability and Gas Barrier in Hydrogen-Bonded Multilayer Nanobrick Wall Thin Films

Hydrogen-bonded multilayer thin films are very stretchable, but their gas barrier properties are modest compared to more traditional ionically bonded assemblies. In an effort to improve the gas barrier of poly(ethylene oxide) (PEO)-poly(acrylic acid) (PAA) multilayer films without sacrificing stretchability, montmorillonite (MMT) clay platelets were combined with PAA and alternately deposited with PEO. A ten-bilayer PEO/PAA+MMT film (432 nm thick), deposited on a 1 mm PU substrate, resulted in a 54× reduction in oxygen transmission rate after exposure to a 20% strain. This system is the best combination of stretchability and gas barrier ever reported.

Molecular Dynamics Simulations of Glycerol Monooleate Confined between Mica Surfaces

The structure and frictional properties of glycerol monooleate (GMO) in organic solvents, with and without water impurity, confined and sheared between two mica surfaces are examined using molecular dynamics simulations. The structure of the fluid is characterized in various ways, and the differences between systems with nonaggregated GMO and with preformed GMO reverse micelles are examined. Preformed reverse micelles are metastable under static conditions in all systems. In n-heptane under shear conditions, with or without water, preformed GMO reverse micelles remain intact and adsorb onto one surface or another, becoming surface micelles. In dry toluene, preformed reverse micelles break apart under shear, while in the presence of water, the reverse micelles survive and become surface micelles. In all systems under static and shear conditions, nonaggregated GMO adsorbs onto both surfaces with roughly equal probability. Added water is strongly associated with the GMO, irrespective of shear or the form of the added GMO. In all cases, with increasing shear rate, the GMO molecules flatten on the surface, and the kinetic friction coefficient increases. Under low-shear conditions, the friction is insensitive to the form of the GMO added, whereas the presence of water is found to lead to a small reduction in friction. Under high-shear conditions, the presence of reverse micelles leads to a significant reduction in friction, whereas the presence of water increases the friction in n-heptane and decreases the friction in toluene.

Dynamics of Seeded Aβ40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step

Filamentous β-amyloid aggregates are crucial for the pathology of Alzheimer's disease. Despite the tremendous biomedical importance, the molecular pathway of growth propagation is not completely understood and remains challenging to investigate by simulations due to the long time scales involved. Here, we apply extensive all-atom molecular dynamics simulations in explicit water to obtain free energy profiles and kinetic information from position-dependent diffusion profiles for three different Aβ9-40-growth processes: fibril elongation by single monomers at the structurally unequal filament tips and association of larger filament fragments. Our approach provides insight into the molecular steps of the kinetic pathway and allows close agreement with experimental binding free energies and macroscopic growth rates. Water plays a decisive role, and solvent entropy is identified as the main driving force for assembly. Fibril growth is disfavored energetically due to cancellation of direct peptide-peptide interactions and solvation effects. The kinetics of growth is consistent with the characteristic dock/lock mechanism, and docking is at least 2 orders of magnitude faster. During initial docking, interactions are mediated by transient non-native hydrogen bonds, which efficiently catch the incoming monomer or fragment already at separations of about 3 nm. In subsequent locking, the dynamics is much slower due to formation of kinetically trapped conformations caused by long-lived non-native hydrogen bonds. Fibril growth additionally requires collective motion of water molecules to create a dry binding interface. Fibril growth is further retarded due to reduced mobility of the involved hydration water, evident from a 2-fold reduction of the diffusion coefficient.

Unfolding and folding internal friction of β-hairpins is smaller than that of α-helices

By the forced unfolding of polyglutamine and polyalanine homopeptides in competing α-helix and β-hairpin secondary structures, we disentangle equilibrium free energetics from nonequilibrium dissipative effects. We find that α-helices are characterized by larger friction or dissipation upon unfolding, regardless of whether they are free energetically preferred over β-hairpins or not. Our analysis, based on MD simulations for atomistic peptide models with explicit water, suggests that this difference is related to the internal friction and mostly caused by the different number of intrapeptide hydrogen bonds in the α-helix and β-hairpin states.

Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution

Ring-shaped, hexameric ATPase motors fulfill key functions in cellular processes, such as genome replication, transcription, or protein degradation, by translocating a long substrate through their central pore powered by ATP hydrolysis. Despite intense research efforts, the atomic-level mechanism transmitting chemical energy from hydrolysis into mechanical force that translocates the substrate is still unclear. Here we employ all-atom molecular dynamics simulations combined with advanced path sampling techniques and milestoning analysis to characterize how mRNA substrate is translocated by an exemplary homohexameric motor, the transcription termination factor Rho. We find that the release of hydrolysis product (ADP + Pi) triggers the force-generating process of Rho through a 0.1 millisecond-long conformational transition, the time scale seen also in experiment. The calculated free energy profiles and kinetics show that Rho unidirectionally translocates the single-stranded RNA substrate via a population shift of the conformational states of Rho; upon hydrolysis product release, the most favorable conformation shifts from the pretranslocation state to the post-translocation state. Via two previously unidentified intermediate states, the RNA chain is seen to be pulled by six K326 side chains, whose motions are induced by highly coordinated relative translation and rotation of Rho's six subunits. The present study not only reveals in new detail the mechanism employed by ring-shaped ATPase motors, for example the use of loosely bound and tightly bound hydrolysis reactant and product states to coordinate motor action, but also provides an effective approach to identify allosteric sites of multimeric enzymes in general.

A molecular view of the role of chirality in charge-driven polypeptide complexation

Polyelectrolyte molecules of opposite charge are known to form stable complexes in solution. Depending on the system conditions, such complexes can be solid or liquid. The latter are known as complex coacervates, and they appear as a second liquid phase in equilibrium with a polymer-dilute aqueous phase. This work considers the complexation between poly(glutamic acid) and poly(lysine), which is of particular interest because it enables examination of the role of chirality in ionic complexation, without changes to the overall chemical composition. Systematic atomic-level simulations are carried out for chains of poly(glutamic acid) and poly(lysine) with varying combinations of chirality along the backbone. Achiral chains form unstructured complexes. In contrast, homochiral chains lead to formation of stable β-sheets between molecules of opposite charge, and experiments indicate that β-sheet formation is correlated with the formation of solid precipitates. Changes in chirality along the peptide backbone are found to cause "kinks" in the β-sheets. These are energetically unfavorable and result in irregular structures that are more difficult to pack together. Taken together, these results provide new insights that may be of use for the development of simple yet strong bioinspired materials consisting of β-rich domains and amorphous regions.

Rate-dependent behavior of the amorphous phase of spider dragline silk

The time-dependent stress-strain behavior of spider dragline silk was already observed decades ago, and has been attributed to the disordered sequences in silk proteins, which compose the soft amorphous matrix. However, the actual molecular origin and magnitude of internal friction within the amorphous matrix has remained inaccessible, because experimentally decomposing the mechanical response of the amorphous matrix from the embedded crystalline units is challenging. Here, we used atomistic molecular dynamics simulations to obtain friction forces for the relative sliding of peptide chains of Araneus diadematus spider silk within bundles of these chains as a representative unit of the amorphous matrix in silk fibers. We computed the friction coefficient and coefficient of viscosity of the amorphous phase to be in the order of 10(-6) Ns/m and 10(4) Ns/m(2), respectively, by extrapolating our simulation data to the viscous limit. Finally, we used a finite element method for the amorphous phase, solely based on parameters derived from molecular dynamics simulations including the newly determined coefficient of viscosity. With this model the time scales of stress relaxation, creep, and hysteresis were assessed, and found to be in line with the macroscopic time-dependent response of silk fibers. Our results suggest the amorphous phase to be the primary source of viscosity in silk and open up the avenue for finite element method studies of silk fiber mechanics including viscous effects.

Detachment of semiflexible polymer chains from a substrate: a molecular dynamics investigation

Using Molecular Dynamics simulations, we study the force-induced detachment of a coarse-grained model polymer chain from an adhesive substrate. One of the chain ends is thereby pulled at constant speed off the attractive substrate and the resulting saw-tooth profile of the measured mean force ⟨f⟩ vs height D of the end-segment over the plane is analyzed for a broad variety of parameters. It is shown that the observed characteristic oscillations in the ⟨f⟩-D profile depend on the bending and not on the torsional stiffness of the detached chains. Allowing for the presence of hydrodynamic interactions (HI) in a setup with explicit solvent and dissipative particle dynamics-thermostat, rather than the case of Langevin thermostat, one finds that HI have little effect on the ⟨f⟩-D profile. Also the change of substrate affinity with respect to the solvent from solvophilic to solvophobic is found to play negligible role in the desorption process. In contrast, a changing ratio ε(s)(B)/ε(s)(A) of the binding energies of A- and B-segments in the detachment of an AB-copolymer from adhesive surface strongly changes the ⟨f⟩-D profile whereby the B-spikes vanish when ε(s)(B)/ε(s)(A)<0.15. Eventually, performing an atomistic simulation of (bio)-polymers, we demonstrate that the simulation results, derived from our coarse-grained model, comply favorably with those from the all-atom simulation.

Viscous friction between crystalline and amorphous phase of dragline silk

The hierarchical structure of spider dragline silk is composed of two major constituents, the amorphous phase and crystalline units, and its mechanical response has been attributed to these prime constituents. Silk mechanics, however, might also be influenced by the resistance against sliding of these two phases relative to each other under load. We here used atomistic molecular dynamics (MD) simulations to obtain friction forces for the relative sliding of the amorphous phase and crystalline units of Araneus diadematus spider silk. We computed the coefficient of viscosity of this interface to be in the order of 10(2) Ns/m(2) by extrapolating our simulation data to the viscous limit. Interestingly, this value is two orders of magnitude smaller than the coefficient of viscosity within the amorphous phase. This suggests that sliding along a planar and homogeneous surface of straight polyalanine chains is much less hindered than within entangled disordered chains. Finally, in a simple finite element model, which is based on parameters determined from MD simulations including the newly deduced coefficient of viscosity, we assessed the frictional behavior between these two components for the experimental range of relative pulling velocities. We found that a perfectly relative horizontal motion has no significant resistance against sliding, however, slightly inclined loading causes measurable resistance. Our analysis paves the way towards a finite element model of silk fibers in which crystalline units can slide, move and rearrange themselves in the fiber during loading.

Confinement-dependent friction in peptide bundles

Friction within globular proteins or between adhering macromolecules crucially determines the kinetics of protein folding, the formation, and the relaxation of self-assembled molecular systems. One fundamental question is how these friction effects depend on the local environment and in particular on the presence of water. In this model study, we use fully atomistic MD simulations with explicit water to obtain friction forces as a single polyglycine peptide chain is pulled out of a bundle of k adhering parallel polyglycine peptide chains. The whole system is periodically replicated along the peptide axes, so a stationary state at prescribed mean sliding velocity V is achieved. The aggregation number is varied between k = 2 (two peptide chains adhering to each other with plenty of water present at the adhesion sites) and k = 7 (one peptide chain pulled out from a close-packed cylindrical array of six neighboring peptide chains with no water inside the bundle). The friction coefficient per hydrogen bond, extrapolated to the viscous limit of vanishing pulling velocity V → 0, exhibits an increase by five orders of magnitude when going from k = 2 to k = 7. This dramatic confinement-induced friction enhancement we argue to be due to a combination of water depletion and increased hydrogen-bond cooperativity.

Single molecule unfolding and stretching of protein domains inside a solid-state nanopore by electric field

Single molecule methods have provided a significantly new look at the behavior of biomolecules in both equilibrium and non-equilibrium conditions. Most notable are the stretching experiments performed by atomic force microscopes and laser tweezers. Here we present an alternative single molecule method that can unfold a protein domain, observed at electric fields greater than 10(6) V/m, and is fully controllable by the application of increasing voltages across the membrane of the pore. Furthermore this unfolding mechanism is characterized by measuring both the residence time of the protein within the nanopore and the current blockade. The unfolding data supports a gradual unfolding mechanism rather than the cooperative transition observed by classical urea denaturation experiments. Lastly it is shown that the voltage-mediated unfolding is a function of the stability of the protein by comparing two mutationally destabilized variants of the protein.

On the relationship between peptide adsorption resistance and surface contact angle: a combined experimental and simulation single-molecule study

The force-induced desorption of single peptide chains from mixed OH/CH(3)-terminated self-assembled monolayers is studied in closely matched molecular dynamics simulations and atomic force microscopy experiments with the goal to gain microscopic understanding of the transition between peptide adsorption and adsorption resistance as the surface contact angle is varied. In both simulations and experiments, the surfaces become adsorption resistant against hydrophilic as well as hydrophobic peptides when their contact angle decreases below θ ≈ 50°-60°, thus confirming the so-called Berg limit established in the context of protein and cell adsorption. Entropy/enthalpy decomposition of the simulation results reveals that the key discriminator between the adsorption of different residues on a hydrophobic monolayer is of entropic nature and thus is suggested to be linked to the hydrophobic effect. By pushing a polyalanine peptide onto a polar surface, simulations reveal that the peptide adsorption resistance is caused by the strongly bound water hydration layer and characterized by the simultaneous gain of both total entropy in the system and total number of hydrogen bonds between water, peptide, and surface. This mechanistic insight into peptide adsorption resistance might help to refine design principles for anti-fouling surfaces.

Structure and mechanical properties of human trichocyte keratin intermediate filament protein

Keratin is a protein in the intermediate filament family and the key component of hair, nail, and skin. Here we report a bottom-up atomistic model of the keratin dimer, using the complete human keratin type k35 and k85 amino acid sequence. A detailed analysis of geometric and mechanical properties through full-atomistic simulation with validation against experimental results is presented. We introduce disulfide cross-links in a keratin tetramer and compare the mechanical behavior of the disulfide bonded systems with a system without disulfide bonds. Disulfide bond results in a higher strength (20% increase) and toughness (49% increase), but the system loses α-helical structures under loading, suggesting that disulfide bonds play a significant role in achieving the characteristic mechanical properties of trichocyte α-keratin. Our study provides general insight into the effect of disulfide cross-link on mechanical properties. Moreover, the availability of an atomistic model of this protein opens the possibility to study the mechanical properties of hair fibrils and other fibers from a bottom-up perspective.