Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interprete atomic force microscopy observations

Contribution of Hydrophobic Interactions to Protein Mechanical Stability

The role of hydrophobic and polar interactions in providing thermodynamic stability to folded proteins has been intensively studied, but the relative contribution of these interactions to the mechanical stability is less explored. We used steered molecular dynamics simulations with constant-velocity pulling to generate force-extension curves of selected protein domains and monitor hydrophobic surface unravelling upon extension. Hydrophobic contribution was found to vary between one fifth and one third of the total force while the rest of the contribution is attributed primarily to hydrogen bonds. Moreover, hydrophobic force peaks were shifted towards larger protein extensions with respect to the force peaks attributed to hydrogen bonds. The higher importance of hydrogen bonds compared to hydrophobic interactions in providing mechanical resistance is in contrast with the relative importance of the hydrophobic interactions in providing thermodynamic stability of proteins. The different contributions of these interactions to the mechanical stability are explained by the steeper free energy dependence of hydrogen bonds compared to hydrophobic interactions on the relative positions of interacting atoms. Comparative analyses for several protein domains revealed that the variation of hydrophobic forces is modest, while the contribution of hydrogen bonds to the force peaks becomes increasingly important for mechanically resistant protein domains.

Steered molecular dynamics simulations reveal the role of Ca2+ in regulating mechanostability of cellulose-binding proteins

The conversion of cellulosic biomass into biofuels requires degradation of the biomass into fermentable sugars. The most efficient natural cellulase system for carrying out this conversion is an extracellular multi-enzymatic complex named the cellulosome. In addition to temperature and pH stability, mechanical stability is important for functioning of cellulosome domains, and experimental techniques such as Single Molecule Force Spectroscopy (SMFS) have been used to measure the mechanical strength of several cellulosomal proteins. Molecular dynamics computer simulations provide complementary atomic-resolution quantitative maps of domain mechanical stability for identification of experimental leads for protein stabilization. In this study, we used multi-scale steered molecular dynamics computer simulations, benchmarked against new SMFS measurements, to measure the intermolecular contacts that confer high mechanical stability to a family 3 Carbohydrate Binding Module protein (CBM3) derived from the archetypal Clostridium thermocellum cellulosome. Our data predicts that electrostatic interactions in the calcium binding pocket modulate the mechanostability of the cellulose-binding module, which provides an additional design rule for the rational re-engineering of designer cellulosomes for biotechnology. Our data offers new molecular insights into the origins of mechanostability in cellulose binding domains and gives leads for synthesis of more robust cellulose-binding protein modules. On the other hand, simulations predict that insertion of a flexible strand can promote alternative unfolding pathways and dramatically reduce the mechanostability of the carbohydrate binding module, which gives routes to rational design of tailormade fingerprint complexes for force spectroscopy experiments.

Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes

Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered molecular dynamics (SMD) to assess the strength of protein-peptide interactions. The idea behind using SMD simulations is that the mechanical stability can be used as a promising and an efficient alternative to computationally highly demanding estimation of binding affinity. However, mechanical stability defined as a peak in force-extension profile depends on the choice of the pulling direction. Here we propose an uncommon choice of the pulling direction along resultant dipole moment (RDM) vector, which has not been explored in SMD simulations so far. Using explicit solvent all-atom MD simulations, we apply SMD technique to probe mechanical resistance of ligand-receptor system pulled along two different vectors. A novel pulling direction—when ligand unbinds along the RDM vector—results in stronger forces compared to commonly used ligand unbinding along center of masses vector. Our observation that RDM is one of the factors influencing the mechanical stability of protein-peptide complex can be used to improve the ranking of binding affinities by using mechanical stability as an effective scoring function.

Structural-elastic determination of the force-dependent transition rate of biomolecules

The force-dependent unfolding/refolding of protein domains and ligand-receptor association/dissociation are crucial for mechanosensitive functions, while many aspects of how force affects the transition rate still remain poorly understood. Here, we report a new analytical expression of the force-dependent rate of molecules for transitions overcoming a single barrier. Unlike previous models derived in the framework of Kramers theory that requires a presumed one-dimensional free energy landscape, our model is derived based on the structural-elastic properties of molecules which are not restricted by the shape and dimensionality of the underlying free energy landscape. Importantly, the parameters of this model provide direct information on the structural-elastic features of the molecules between their transition and initial states. We demonstrate the applications of this model by applying it to explain force-dependent transition kinetics for several molecules and predict the structural-elastic properties of the transition states of these molecules.

Discriminating Residue Substitutions in a Single Protein Molecule Using a Sub-nanopore

It is now possible to create, in a thin inorganic membrane, a single, sub-nanometer-diameter pore (i.e., a sub-nanopore) about the size of an amino acid residue. To explore the prospects for sequencing protein with it, measurements of the force and current were performed as two denatured histones, which differed by four amino acid residue substitutions, were impelled systematically through the sub-nanopore one at a time using an atomic force microscope. The force measurements revealed that once the denatured protein, stabilized by sodium dodecyl sulfate (SDS), translocated through the sub-nanopore, a disproportionately large force was required to pull it back. This was interpreted to mean that the SDS was cleaved from the protein during the translocation. The force measurements also exposed a dichotomy in the translocation kinetics: either the molecule slid nearly frictionlessly through the pore or it slipped-and-stuck. When it slid frictionlessly, regardless of whether the molecule was pulled N-terminus or C-terminus first through the pore, regular patterns were observed intermittently in the force and blockade current fluctuations that corresponded to the distance between stretched residues. Furthermore, the amplitude of the fluctuations in the current blockade were correlated with the occluded volume associated with the amino acid residues in the pore. Finally, a comparison of the patterns in the current fluctuations associated with the two practically identical histones supported the conclusion that a sub-nanopore was sensitive enough to discriminate amino acid substitutions in the sequence of a single protein molecule by measuring volumes of 0.1 nm³ per read.

Perspective: Mechanochemistry of biological and synthetic molecules

Coupling of mechanical forces and chemical transformations is central to the biophysics of molecular machines, polymer chemistry, fracture mechanics, tribology, and other disciplines. As a consequence, the same physical principles and theoretical models should be applicable in all of those fields; in fact, similar models have been invoked (and often repeatedly reinvented) to describe, for example, cell adhesion, dry and wet friction, propagation of cracks, and action of molecular motors. This perspective offers a unified view of these phenomena, described in terms of chemical kinetics with rates of elementary steps that are force dependent. The central question is then to describe how the rate of a chemical transformation (and its other measurable properties such as the transition path) depends on the applied force. I will describe physical models used to answer this question and compare them with experimental measurements, which employ single-molecule force spectroscopy and which become increasingly common. Multidimensionality of the underlying molecular energy landscapes and the ensuing frequent misalignment between chemical and mechanical coordinates result in a number of distinct scenarios, each showing a nontrivial force dependence of the reaction rate. I will discuss these scenarios, their commonness (or its lack), and the prospects for their experimental validation. Finally, I will discuss open issues in the field.

Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis

In quantum mechanochemistry, quantum chemical methods are used to describe molecules under the influence of an external force. The calculation of geometries, energies, transition states, reaction rates, and spectroscopic properties of molecules on the force-modified potential energy surfaces is the key to gain an in-depth understanding of mechanochemical processes at the molecular level. In this review, we present recent advances in the field of quantum mechanochemistry and introduce the quantum chemical methods used to calculate the properties of molecules under an external force. We place special emphasis on quantum chemical force analysis tools, which can be used to identify the mechanochemically relevant degrees of freedom in a deformed molecule, and spotlight selected applications of quantum mechanochemical methods to point out their synergistic relationship with experiments.

Nanomechanical properties of MscL α helices: A steered molecular dynamics study

Gating of mechanosensitive (MS) channels is driven by a hierarchical cascade of movements and deformations of transmembrane helices in response to bilayer tension. Determining the intrinsic mechanical properties of the individual transmembrane helices is therefore central to understanding the intricacies of the gating mechanism of MS channels. We used a constant-force steered molecular dynamics (SMD) approach to perform unidirectional pulling tests on all the helices of MscL in M. tuberculosis and E. coli homologs. Using this method, we could overcome the issues encountered with the commonly used constant-velocity SMD simulations, such as low mechanical stability of the helix during stretching and high dependency of the elastic properties on the pulling rate. We estimated Young's moduli of the α-helices of MscL to vary between 0.2 and 12.5 GPa with TM2 helix being the stiffest. We also studied the effect of water on the properties of the pore-lining TM1 helix. In the absence of water, this helix exhibited a much stiffer response. By monitoring the number of hydrogen bonds, it appears that water acts like a 'lubricant' (softener) during TM1 helix elongation. These data shed light on another physical aspect underlying hydrophobic gating of MS channels, in particular MscL.

Steered molecular dynamics study reveals insights into the function of the repetitive B region of collagen- and fibrinogen-binding MSCRAMMs

MSCRAMMs (microbial surface components recognizing adhesive matrix molecules) are modular proteins covalently anchored in the bacterial cell wall of many Gram-positive bacteria. The N-terminal region of most MSCRAMMs carries the ligand-binding domains (A region) which specifically target the host extracellular matrix (ECM) proteins such as collagen, fibrinogen and fibronectin. In Staphylococcus aureus Cna, the prototype collagen-binding MSCRAMM, the A region is followed by a repetitive B region which is found to be conserved among many Gram-positive bacteria. This conservation signifies an important functional role for the B region which is made of repetitive domains. It was suggested that this region could act as a 'stalk' as well as a 'spring' to present the ligand-binding A region, away from the bacterial surface. But there is no clear functional implication of this region available till date. Each repetitive domain in the B region possesses a variant of the Ig fold called the CnaB fold. Additionally, the B repeats are also paired and the pairs are clustered together. To investigate if the B domains have a function similar to the Ig domains in the I-band region of the giant muscle protein, titin, steered molecular dynamics simulations of one, two and four B repeats of Cna were carried out. The results of the simulations suggest that the B region could provide mechanical stability, extensibility and elasticity to Cna due to the CnaB fold as well as the clustered arrangement of their domains. This study thus provided further insights into the biological underpinnings of adhesin-host interaction.

The role of sequence in altering the unfolding pathway of an RNA pseudoknot: a steered molecular dynamics study

This work highlights a sequence dependent unfolding pathway of an RNA pseudoknot under force-induced pulling conditions.

Exploring the topography of the stress-modified energy landscapes of mechanosensitive molecules

We propose a method for computing the activation barrier for chemical reactions involving molecules subjected to mechanical stress. The method avoids reactant and transition-state saddle optimizations at every force by, instead, solving the differential equations governing the force dependence of the critical points (i.e., minima and saddles) on the system's potential energy surface (PES). As a result, only zero-force geometry optimization (or, more generally, optimization performed at a single force value) is required by the method. In many cases, minima and transition-state saddles only exist within a range of forces and disappear beyond a certain critical point. Our method identifies such force-induced instabilities as points at which one of the Hessian eigenvalues vanishes. We elucidate the nature of those instabilities as fold and cusp catastrophes, where two or three critical points on the force-modified PES coalesce, and provide a classification of various physically distinct instability scenarios, each illustrated with a concrete chemical example.

A structure-based model fails to probe the mechanical unfolding pathways of the titin I27 domain

We discuss the use of a structure based Cα-Go model and Langevin dynamics to study in detail the mechanical properties and unfolding pathway of the titin I27 domain. We show that a simple Go-model does detect correctly the origin of the mechanical stability of this domain. The unfolding free energy landscape parameters x(u) and ΔG(‡), extracted from dependencies of unfolding forces on pulling speeds, are found to agree reasonably well with experiments. We predict that above v = 10(4) nm/s the additional force-induced intermediate state is populated at an end-to-end extension of about 75 Å. The force-induced switch in the unfolding pathway occurs at the critical pulling speed v(crit) ≈ 10(6)-10(7) nm/s. We argue that this critical pulling speed is an upper limit of the interval where Bell's theory works. However, our results suggest that the Go-model fails to reproduce the experimentally observed mechanical unfolding pathway properly, yielding an incomplete picture of the free energy landscape. Surprisingly, the experimentally observed intermediate state with the A strand detached is not populated in Go-model simulations over a wide range of pulling speeds. The discrepancy between simulation and experiment is clearly seen from the early stage of the unfolding process which shows the limitation of the Go model in reproducing unfolding pathways and deciphering the complete picture of the free energy landscape.

On the improvement of free-energy calculation from steered molecular dynamics simulations using adaptive stochastic perturbation protocols

The potential of mean force (PMF) calculation in single molecule manipulation experiments performed via the steered molecular dynamics (SMD) technique is a computationally very demanding task because the analyzed system has to be perturbed very slowly to be kept close to equilibrium. Faster perturbations, far from equilibrium, increase dissipation and move the average work away from the underlying free energy profile, and thus introduce a bias into the PMF estimate. The Jarzynski equality offers a way to overcome the bias problem by being able to produce an exact estimate of the free energy difference, regardless of the perturbation regime. However, with a limited number of samples and high dissipation the Jarzynski equality also introduces a bias. In our previous work, based on the Brownian motion formalism, we introduced three stochastic perturbation protocols aimed at improving the PMF calculation with the Jarzynski equality in single molecule manipulation experiments and analogous computer simulations. This paper describes the PMF reconstruction results based on full-atom molecular dynamics simulations, obtained with those three protocols. We also want to show that the protocols are applicable with the second-order cumulant expansion formula. Our protocols offer a very noticeable improvement over the simple constant velocity pulling. They are able to produce an acceptable estimate of PMF with a significantly reduced bias, even with very fast perturbation regimes. Therefore, the protocols can be adopted as practical and efficient tools for the analysis of mechanical properties of biological molecules.

Nanomechanics of β-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods

Computer simulations of protein unfolding substantially help to interpret force-extension curves measured in single-molecule atomic force microscope (AFM) experiments. Standard all-atom (AA) molecular dynamics simulations (MD) give a good qualitative mechanical unfolding picture but predict values too large for the maximum AFM forces with the common pulling speeds adopted here. Fine tuned coarse-grain MD computations (CG MD) offer quantitative agreement with experimental forces. In this paper we address an important methodological aspect of MD modeling, namely the impact of numerical noise generated by random assignments of bead velocities on maximum forces (F_max) calculated within the CG MD approach. Distributions of CG forces from 2000 MD runs for several model proteins rich in β structures and having folds with increasing complexity are presented. It is shown that F_max have nearly Gaussian distributions and that values of F_max for each of those β-structures may vary from 93.2 ± 28.9 pN (neurexin) to 198.3 ± 25.2 pN (fibronectin). The CG unfolding spectra are compared with AA steered MD data and with results of our AFM experiments for modules present in contactin, fibronectin and neurexin. The stability of these proteins is critical for the proper functioning of neuronal synaptic clefts. Our results confirm that CG modeling of a single molecule unfolding is a good auxiliary tool in nanomechanics but large sets of data have to be collected before reliable comparisons of protein mechanical stabilities are made.

Figure

Topological features in stretching of proteins

In the present article, we highlight the diversity of mechanical clamps, some of them topological in nature, that have been found by making surveys of mechanostability of approximately 18000 proteins within structure-based models. The existence of superstable proteins (with the characteristic unfolding force in the region of 1000 pN) is predicted.

Pulling-spring modulation as a method for improving the potential-of-mean-force reconstruction in single-molecule manipulation experiments

The free-energy calculation is usually limited to close to equilibrium perturbation regimes because faster perturbations introduce a bias into the estimate. The Jarzynski equality offers a solution to this problem by directly connecting the free-energy difference and the external work, regardless how far from equilibrium that work may be. However, a limited sampling coupled to the fast perturbation introduces a slowly converging bias into the Jarzynski free-energy estimate also. In this paper we present two perturbation protocols devised with the intention to overcome the convergence issues of the Jarzynski-based potential of mean force estimation in the single-molecule, constant velocity manipulation experiments. The protocols are designed to improve the convergence issues by increasing the variation of the external work through the modulation of the spring used to pull a molecule. Of the two methods, the one which continuously changes the amplitude of the spring stiffness offers an excellent reconstruction and requires less than one tenth of the samples required by the normal, constant spring pulling to produce the same quality of the reconstruction.

Using simulations to provide the framework for experimental protein folding studies

Molecular dynamics simulations are a powerful theoretical tool to model the protein folding process in atomistic details under realistic conditions. Combined with a number of experimental techniques, simulations provide a detailed picture of how a protein folds or unfolds in the presence of explicit solvent and other molecular species, such as cosolvents, osmolytes, cofactors, active binding partners or inert crowding agents. The denaturing effects of temperature, pressure and external mechanical forces can also be probed. Qualitative and quantitative agreement with experiment contributes to a comprehensive molecular picture of protein states along the folding/unfolding pathway. The variety of systems examined reveals key features of the protein folding process.

The role of domain: domain interactions versus domain: water interactions in the coarse-grained simulations of the E1P to E2P transitions in Ca-ATPase (SERCA)

SERCA is an important model system for understanding the molecular details of conformational change in membrane transport systems. This reflects the large number of solved X-ray structures and the equally large database of mutations that have been assayed. In this computational study, we provide a molecular dynamics description of the conformational changes during the E1P → E2P transitions. This set of states further changes with insertion mutants in the A-M3 linker region. These mutants were experimentally shown to lead to significant shifts in rates between the E1P → E2P states. Using the population shift framework and dynamic importance sampling method along with coarse-grained representations of the protein, lipid, and water, we suggest why these changes are found. The calculations sample on intermediates and suggest that changes in interactions, individual helix interactions, and water behavior are key elements in the molecular compositions that underlie shifts in kinetics. In particular, as the insertion length grows, it attracts more water and disrupts domain interactions, creating changes as well at the sites of key helix interactions between the A-Domain and the P-Domain. This provides a conceptual picture that aids understanding of the experimental results.

Computational investigation of the effect of thermal perturbation on the mechanical unfolding of titin I27

The emergence of single-molecule force measurement experiments has facilitated a better understanding of protein folding pathways and the thermodynamics involved. Computational methods such as steered molecular dynamics (SMD) simulations are helpful in providing atomistic level information on the unfolding pathways. Recent experimental studies have showed that combinations of single-molecule experiments with traditional methods such as chemical and/or thermal denaturation yield additional insights into the folding phenomenon. In this study, we report results from extensive computations (a total of about 60 SMD simulations with a total length of about 0.4 μs) that address the effect of thermal perturbation on the mechanical stability of the I27 domain of the protein titin. A wide range of temperatures (280-340 K) were considered for the pulling, which was done at both constant velocity and constant force using SMD simulations. Good agreement with experimental data, such as for the trends in changes in average force and the maximum force with respect to the temperature, was obtained. This study identifies two competing pathways for the mechanical unfolding of I27, and illustrates the significance of combining various techniques to examine protein folding.

Efficient free-energy-profile reconstruction using adaptive stochastic perturbation protocols

The Jarzynski-relation-based free-energy calculation is limited by the very slow convergence of the estimate when dissipation is high. We present two novel perturbation protocols able to significantly improve the quality of the potential of mean force (PMF) calculation by reducing the estimate's bias without increasing the number of samples. The protocols are directly applicable with both numerical simulations and real-life experiments. The improvement is achieved through the intentional but controlled widening of the distribution of the external work used to perturb a given system. Our protocols can achieve the same accuracy in PMF estimation as the normal constant velocity pulling with less than 10% of the required samples.

Molecular jamming--the cystine slipknot mechanical clamp in all-atom simulations

A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids.

Influence of external force on properties and reactivity of disulfide bonds

The mechanochemistry of the disulfide bridge--that is, the influence of an externally applied force on the reactivity of the sulfur-sulfur bond--is investigated by unrestricted Kohn-Sham theory. Specifically, we apply the COGEF (constrained geometry simulates external force) approach to characterize the mechanochemistry of the disulfide bond in three different chemical environments: dimethyl disulfide, cystine, and a 102-atom model of the I27 domain in the titin protein. Furthermore, the mechanism of the thiol-disulfide reduction reaction under the effect of an external force is investigated by considering the COGEF potential for the adduct and transition-state clusters. With the unrestricted Becke-three-parameter-Lee-Yang-Parr (UB3LYP) exchange-correlation functional in the 6-311++G(3df,3pd) orbital basis, the rupture force of dimethyl disulfide is 3.8 nN at a disulfide bond elongation of 35 pm. The interaction with neighboring groups and the effect of conformational rigidity of the protein environment have little influence on the mechanochemical characteristics. Upon stretching, we make the following observations: the diradical character of the disulfide bridge increases; the energy difference between the singlet ground state and low-lying triplet state decreases; and the disulfide reduction is promoted by an external force in the range 0.1-0.4 nN. Our model of the interplay between force and reaction mechanism is in qualitative agreement with experimental observations.

Molecular motions in drug design: the coming age of the metadynamics method

Metadynamics is emerging as a useful free energy method in physics, chemistry and biology. Recently, it has been applied also to investigate ligand binding to biomolecules of pharmacological interest. Here, after introducing the basic idea of the method, we review applications to challenging targets for pharmaceutical intervention. We show that this methodology, especially when combined with a variety of other computational approaches such as molecular docking and/or molecular dynamics simulation, may be useful to predict structure and energetics of ligand/target complexes even when the targets lack a deep binding cavity, such as DNA and proteins undergoing fibrillation in neurodegenerative diseases. Furthermore, the method allows investigating the routes of molecular recognition and the associated binding energy profiles, providing a molecular interpretation to experimental data.

Water's role in the force-induced unfolding of ubiquitin

In atomic force spectroscopic studies of the elastomeric protein ubiquitin, the β-strands 1-5 serve as the force clamp. Simulations show how the rupture force in the force-induced unfolding depends on the kinetics of water molecule insertion into positions where they can eventually form hydrogen bonding bridges with the backbone hydrogen bonds in the force-clamp region. The intrusion of water into this region is slowed down by the hydrophobic shielding effect of carbonaceous groups on the surface residues of β-strands 1-5, which thereby regulates water insertion prior to hydrogen bond breakage. The experiments show that the unfolding of the mechanically stressed protein is nonexponential due to static disorder. Our simulations show that different numbers and/or locations of bridging water molecules give rise to a long-lived distribution of transition states and static disorder. We find that slowing down the translational (not rotational) motions of the water molecules by increasing the mass of their oxygen atoms, which leaves the force field and thereby the equilibrium structure of the solvent unchanged, increases the average rupture force; however, the early stages of the force versus time behavior are very similar for our "normal" and fictitious "heavy" water models. Finally, we construct six mutant systems to regulate the hydrophobic shielding effect of the surface residues in the force-clamp region. The mutations in the two termini of β-sheets 1-5 are found to determine a preference for different unfolding pathways and change mutant's average rupture force.

BSDB: the biomolecule stretching database

We describe the Biomolecule Stretching Data Base that has been recently set up at http://www.ifpan.edu.pl/BSDB/. It provides information about mechanostability of proteins. Its core is based on simulations of stretching of 17 134 proteins within a structure-based model. The primary information is about the heights of the maximal force peaks, the force-displacement patterns, and the sequencing of the contact-rupturing events. We also summarize the possible types of the mechanical clamps, i.e. the motifs which are responsible for a protein's resistance to stretching.

Investigation of the binding preference of reovirus sigma1 for junctional adhesion molecule A by classical and steered molecular dynamics

Biochemical studies have determined that reoviruses attach to cells by combining attachment protein sigma1 to the binding interface of its receptor protein junctional adhesion molecule A (JAM-A), and the interface normally takes care of the homodimerization of JAM-A. Tighter binding and slower dissociation of for the sigma1-JAM complex than for the JAM-JAM complex have been probed by both biological and atomic force microscopy experiments; however, the mechanism of the binding preference of the attachment protein for JAM-A still remains unclear. With the help of classical and steered molecular dynamics and energy calculations, the unbinding forces and kinetic properties of the complexes are investigated, together with detailed structural information analyses. A multireceptor mechanism is proposed for the binding preference, which can be helpful for future viral infection and vector targeting studies.

Stretching and twisting of the DNA duplexes in coarse-grained dynamical models

Three coarse-grained molecular dynamics models of the double-stranded DNA are proposed and compared in the context of single molecule mechanical manipulation such as twisting and various schemes of stretching-unzipping, shearing, two-strand stretching and stretching of only one strand. The models differ in the number of effective beads (between two and five) representing each nucleotide. They all show similar behaviour, but the bigger the resolution, the more details in the force patterns. The models incorporate the effective Lennard-Jones potentials in the couplings between two strands and harmonic potentials to describe the structure of a single strand. The force patterns are shown to depend on the sequence studied. In particular, both shearing and unzipping for an all-AT sequence lead to lower forces than for an all-CG sequence. The unzipping patterns and the corresponding scenario diagrams for the contact rupture events are found to reflect the sequential information if the temperature is moderate and initial transients are discarded. The derived torque-force phase diagram is found to be qualitatively consistent with experiments and all-atom simulations.

Polymers in crowded environment under stretching force: Globule-coil transitions

We study flexible polymer macromolecules in a crowded (porous) environment, modeling them as self-attracting self-avoiding walks on site-diluted percolative lattices in space dimensions d=2,3 . The influence of stretching force on the polymer folding and the properties of globule-coil transitions are analyzed. Applying the pruned-enriched Rosenbluth chain-growth method, we estimate the transition temperature TTheta between collapsed and extended polymer configurations and construct the phase diagrams of the globule-coil coexistence when varying temperature and stretching force. The transition to a completely stretched state, caused by applying force, is discussed as well.

Mechanical signaling on the single protein level studied using steered molecular dynamics

Efficient communication between the cell and its external environment is of the utmost importance to the function of multicellular organisms. While signaling events can be generally characterized as information exchange by means of controlled energy conversion, research efforts have hitherto mainly been concerned with mechanisms involving chemical and electrical energy transfer. Here, we review recent computational efforts addressing the function of mechanical force in signal transduction. Specifically, we focus on the role of steered molecular dynamics (SMD) simulations in providing details at the atomic level on a group of protein domains, which play a fundamental role in signal exchange by responding properly to mechanical strain. We start by giving a brief introduction to the SMD technique and general properties of mechanically stable protein folds, followed by specific examples illustrating three general regimes of signal transfer utilizing mechanical energy: purely mechanical, mechanical to chemical, and chemical to mechanical. Whenever possible the physiological importance of the example at hand is stressed to highlight the diversity of the processes in which mechanical signaling plays a key role. We also provide an overview of future challenges and perspectives for this rapidly developing field.

Mechanochemistry: one bond at a time

Single-molecule force-clamp spectroscopy offers a novel platform for mechanically denaturing proteins by applying a constant force to a polyprotein. A powerful emerging application of the technique is that, by introducing a disulfide bond in each protein module, the chemical kinetics of disulfide bond cleavage under different stretching forces can be probed at the single-bond level. Even at forces much lower than that which can rupture the chemical bond, the breaking of the S-S bond at the presence of various chemical reducing agents is significantly accelerated. Our previous work demonstrated that the rate of thiol/disulfide exchange reaction is force-dependent and well-described by an Arrhenius term of the form r = A(exp((FΔx(r) - E(a))/k(B)T)[nucleophile]). From Arrhenius fits to the force dependency of the reduction rate, we measured the bond elongation parameter, Δx(r), along the reaction coordinate to the transition state of the S(N)2 reaction cleaved by different nucleophiles and enzymes, never before observed by any other technique. For S-S cleavage by various reducing agents, obtaining the Δx(r) value can help depicting the energy landscapes and elucidating the mechanisms of the reactions at the single-molecule level. Small nucleophiles, such as 1,4-dl-dithiothreitol (DTT), tris(2-carboxyethyl)phosphine (TCEP), and l-cysteine, react with the S-S bond with monotonically increasing rates under the applied force, while thioredoxin enzymes exhibit both stretching-favored and -resistant reaction-rate regimes. These measurements demonstrate the power of the single-molecule force-clamp spectroscopy approach in providing unprecedented access to chemical reactions.

Mechanical response of silk crystalline units from force-distribution analysis

The outstanding mechanical toughness of silk fibers is thought to be caused by embedded crystalline units acting as cross links of silk proteins in the fiber. Here, we examine the robustness of these highly ordered beta-sheet structures by molecular dynamics simulations and finite element analysis. Structural parameters and stress-strain relationships of four different models, from spider and Bombyx mori silk peptides, in antiparallel and parallel arrangement, were determined and found to be in good agreement with x-ray diffraction data. Rupture forces exceed those of any previously examined globular protein many times over, with spider silk (poly-alanine) slightly outperforming Bombyx mori silk ((Gly-Ala)(n)). All-atom force distribution analysis reveals both intrasheet hydrogen-bonding and intersheet side-chain interactions to contribute to stability to similar extent. In combination with finite element analysis of simplified beta-sheet skeletons, we could ascribe the distinct force distribution pattern of the antiparallel and parallel silk crystalline units to the difference in hydrogen-bond geometry, featuring an in-line or zigzag arrangement, respectively. Hydrogen-bond strength was higher in antiparallel models, and ultimately resulted in higher stiffness of the crystal, compensating the effect of the mechanically disadvantageous in-line hydrogen-bond geometry. Atomistic and coarse-grained force distribution patterns can thus explain differences in mechanical response of silk crystals, opening up the road to predict full fiber mechanics.

A single-molecule perspective on the role of solvent hydrogen bonds in protein folding and chemical reactions

We present an array of force spectroscopy experiments that aim to identify the role of solvent hydrogen bonds in protein folding and chemical reactions at the single-molecule level. In our experiments we control the strength of hydrogen bonds in the solvent environment by substituting water (H(2)O) with deuterium oxide (D(2)O). Using a combination of force protocols, we demonstrate that protein unfolding, protein collapse, protein folding and a chemical reaction are affected in different ways by substituting H(2)O with D(2)O. We find that D(2)O molecules form an integral part of the unfolding transition structure of the immunoglobulin module of human cardiac titin, I27. Strikingly, we find that D(2)O is a worse solvent than H(2)O for the protein I27, in direct contrast with the behaviour of simple hydrocarbons. We measure the effect of substituting H(2)O with D(2)O on the force dependent rate of reduction of a disulphide bond engineered within a single protein. Altogether, these experiments provide new information on the nature of the underlying interactions in protein folding and chemical reactions and demonstrate the power of single-molecule techniques to identify the changes induced by a small change in hydrogen bond strength.

Blocking of carbon nanotube based nanoinjectors by lipids: a simulation study

Carbon nanotubes (CNTs) are possible nanoinjectors for the introduction of therapeutic agents into cells. To explore their interactions with a lipid bilayer membrane and to model the nanoinjection process, we used coarse-grained molecular dynamics to simulate the penetration of dipalmitoylphosphatidylcholine (DPPC) bilayers by single-walled CNTs. Lipids are extracted from a bilayer during CNT penetration and reside on both the inner and the outer tube surfaces. Lipids that interact with the CNT interior wall spread out and hence can "block" the tube. However, the degree of lipid lining of the inner surface is strongly dependent upon the tube penetration velocity, with fewer lipids extracted from the bilayer at higher rates. There is no apparent effect on bilayer integrity after CNT penetration, with the bilayer able to self-seal. Our findings reveal some of the complexities of the interactions of lipids with CNT nanoinjectors and suggest a need to further characterize the influence of, for example, CNT functionalization and cargo on lipid blocking of CNTs.

Stabilization provided by neighboring strands is critical for the mechanical stability of proteins

Single-molecule force spectroscopy studies and steered molecular dynamics simulations have revealed that protein topology and pulling geometry play important roles in determining the mechanical stability of proteins. Most studies have focused on local interactions that are associated with the force-bearing beta-strands. Interactions mediated by neighboring strands are often overlooked. Here we use Top7 and barstar as model systems to illustrate the critical importance of the stabilization effect provided by neighboring beta-strands on the mechanical stability. Using single-molecule atomic force microscopy, we showed that Top7 and barstar, which have similar topology in their force-bearing region, exhibit vastly different mechanical-stability characteristics. Top7 is mechanically stable and unfolds at approximately 150 pN, whereas barstar is mechanically labile and unfolds largely below 50 pN. Steered molecular dynamics simulations revealed that stretching force peels one force-bearing strand away from barstar to trigger unfolding, whereas Top7 unfolds via a substructure-sliding mechanism. This previously overlooked stabilization effect from neighboring beta-strands is likely to be a general mechanism in protein mechanics and can serve as a guideline for the de novo design of proteins with significant mechanical stability and novel protein topology.