Adhesion from tethered ligand-receptor bonds with microsecond lifetimes

According to classical thermodynamics, biological ligand-receptor bonds should have a median lifetime of about 2 ms, and nearly half should have lifetimes of nanoseconds to microseconds. As a result, it is clear that many "weak" bonds are indispensable for cellular adhesion, signaling, and other critical events. However, the forces required to rupture such weak bonds and the adhesion they provide between surfaces are largely unknown because of their propensity to dissociate rapidly from a measuring probe. To measure such weak bond forces quantitatively, we followed nature's example of adhering surfaces with many weak ligand-receptor bonds. Analogously to how multiplicity promotes stronger adhesion between cellular membranes, multiple bonds created significant adhesion between model cellular surfaces. Specifically, we used an automated surface forces apparatus to measure the adhesion between complementary surfaces bearing dense populations of streptavidin receptors and flexible PEG tethers that each anchored a weakly binding ligand (HABA, or 2-(4-hydroxyphenylazo) benzoic acid). We show that this short-lived bond (<100 mus) leads to low forces of dissociation and only a small fraction being simultaneously bound. These results are significant because the HABA-streptavidin bond energy ( approximately 10.5kBT) is similar to the average found in nature (14.7kBT). The measurements exemplify how a single ligand-receptor bond may fall apart and rejoin many times before completing a cellular function yet can still exhibit strength in numbers.     

Energy landscapes of biomolecular adhesion and receptor anchoring at interfaces explored with dynamic force spectroscopy

Beyond covalent connections within protein and lipid molecules, weak noncovalent interactions between large molecules govern properties of cellular structure and interfacial adhesion in biology. These bonds and structures have limited lifetimes and so will fail under any level of force if pulled on for the right length of time. As such, the strength of interaction is the level of force most likely to disrupt a bond on a particular time scale. For instance, strength is zero on time scales longer than the natural lifetime for spontaneous dissociation. On the other hand, if driven to unbind or change structure on time scales shorter than needed for diffusive relaxation, strength will reach an adiabatic limit set by the maximum gradient in a potential of mean force. Over the enormous span of time scales between spontaneous dissociation and adiabatic detachment, theory predicts that bond breakage under steadily rising force occurs most frequently at a force determined by the rate of loading. Moreover, the continuous plot (spectrum) of strength expressed on a scale of loge(loading rate) provides a map of the prominent barriers traversed in the energy landscape along the force-driven pathway and reveals the differences in energy between barriers. Illustrated with results from recent laboratory measurements, dynamic strength spectra provide a new view into the inner complexity of receptor-ligand interactions and receptor lipid anchoring.     

Molecular bond formation between surfaces: anchoring and shearing effects

Specific molecular bonds between apposing surfaces play a central role in many biological structures and functions. They display a widely varying anchoring to the cell surface, and they are subject to forces that affect their binding characteristics due to their hydrodynamic environments. Here, we examine both anchoring and shearing aspects using simplified model systems aimed at gaining insight into the formation of a 2D bond collection under stress using two different surface anchors. The highly specific streptavidin-biotin molecular bond was chosen as the model receptor-ligand pair, and grafted colloids were used as model surfaces. To explore the role of the surface anchor, we grafted biotin onto the particle surface following two different approaches: first, the grafting was performed directly on the particle amine functions; second, a 35-nm-long PEG spacer was used. Hybrid particle classes were brought into contact in a homogeneous shear (between 200 s(-)(1) and 1200 s(-)(1)) using a cone plate geometry. The bond association and dissociation kinetics were given by the time course assemblage of hybrid particles into doublets. We observed saturating kinetics profiles that we interpreted as a linkage-breakage equilibrium, which yielded the on and off rates. We found that the biotin-PEG spacer was needed in order to observe significant binding at any shear rate. We also showed that only the number of collisions per unit time, generated by the shear, affected the on rate of the binding. Neither the exerted forces nor the collision lifetime had any effect. The off rate decreased with shear, possibly because of the shortening of the force duration, which results from the increasing shear rate.     

The Nature of Activated Non‐classical Hydrogen Bonds: A Case Study on Acetylcholinesterase–Ligand Complexes

Molecular recognition events in biological systems are driven by non‐covalent interactions between interacting species. Here, we have studied hydrogen bonds of the CH???Y type involving electron‐deficient CH donors using dispersion‐corrected density functional theory (DFT) calculations applied to acetylcholinesterase–ligand complexes. The strengths of CH???Y interactions activated by a proximal cation were considerably strong; comparable to or greater than those of classical hydrogen bonds. Significant differences in the energetic components compared to classical hydrogen bonds and non‐activated CH???Y interactions were observed. Comparison between DFT and molecular mechanics calculations showed that common force fields could not reproduce the interaction energy values of the studied hydrogen bonds. The presented results highlight the importance of considering CH???Y interactions when analysing protein–ligand complexes, call for a review of current force fields, and opens up possibilities for the development of improved design tools for drug discovery.     

Combined laser tweezers and dielectric field cage for the analysis of receptor-ligand interactions on single cells

A new technique based on the combination of optical and chip-based dielectrophoretical trapping was developed and employed to manipulate cells and beads with micrometer precision. The beads were trapped with optical tweezers (OT) and brought into contact for defined times with cells held in the dielectrophoretic field cage (DFC). The well-defined ligand-receptor system biotin-streptavidin was used to study the multiple interaction between biotinylated live cells and streptavidin-coated beads. The biotin density on the cell surface was varied down to a few single bonds (3 +/- 2 bonds/microm2) to control the valency of the binding. The quantitative relationship between the contact area, ligand density and its diffusion rate in the outer membrane of the cell could be demonstrated. The increase of the strength of the cell-bead adhesion was strictly dependent on the increase of individual bond numbers in the contact area. This is in part due to accumulation of ligands (D approxiamtely (0.5 +/- 0.1) 10(-8) cm2/s) in the contact area as seen by confocal laser scanning microscopy. Individual receptor-ligand rupture forces were evaluated and are compatible with values obtained by biomembrane force probe techniques. To summarize, the combination leads to a new powerful microsystem for cell handling and pN-force measurements on the single-cell level.     

Mechanopolymerchemie

Although many methods can be employed to transfer energy to a chemical reaction, mechanical energy has not been widely used: It is difficult to apply mechanical forces high enough to lead to breaking bonds to small molecules. Work is the product of force and displacement but when the distances are small, very high forces are needed to obtain sufficient energy to break a bond. The situation is different in polymers, where the path length can be high. Here, bond cleavage, cycloreversions and isomerisations can be observed when mechanical energy is supplied, both in solution and solid systems. Mechanical energy can lead to different mechanistic pathways than those observed under thermal conditions or irradiation. Practical applications of the mechanochemistry of polymers are only just emerging and range from a better understanding of polymer decomposition under force to the development of strain sensors using mechanochromic polymers.     

Influences of linkage stiffness on rupture rate in single-molecule pulling experiments

In the dissociation of a noncovalent biomolecular bond by external pulling, the bonded site is often connected to the force-acting site by a linkage. The role of the linkage stiffness on the rupture of a ligand-receptor complex under constant force is investigated by overdamped Langevin dynamics for the elastically coupled ligand and probe. The effects on the bond lifetime include effective ligand diffusivity, force fluctuations, and violation of adiabatic condition. The rupture rate declines with increasing linkage stiffness. For soft linkage, the effect associated with the spring and probe can be ignored, and the true rupture rate can be extracted. On the other hand, for stiff linkage, the diffusivity of the probe has to be accounted for and, thus, leads to a lower rupture rate, depending on the diffusivity ratio between the probe and ligand. Nevertheless, the energy barrier height can be reasonably extracted by constant pulling experiments, regardless of the linkage stiffness.     

Selective inhibition of engineered receptors via proximity-accelerated alkylation

A new approach for creating allele-specific inhibitors is demonstrated. In this approach, a receptor and ligand are engineered to contain complementary reactive groups that form a covalent bond via a proximity-accelerated reaction upon formation of the receptor-ligand complex, irreversibly modulating the biological function of the receptor. This approach is demonstrated in the cyclophilin-cyclosporin receptor-ligand system by introducing thiol and acrylamide functional groups in the receptor and ligand, respectively.     

Proper and improper hydrogen bonds in liquid water

The total lifetime distributions for hydrogen bonds in snapshots of molecular dynamics simulations of water serve as a basis to identify a class of proper hydrogen bonds. Proper bonds emerge and break up when restructuring the surrounding area of the hydrogen bond networkwhich weakly depend on the properties of this individual bond, i.e., almost randomly. Therefore, the distribution of the bond lifetimes is described by an exponential function similar to the distribution of the mean free path time in gas. It is shown that proper hydrogen bonds are strong, long-lived, and tetrahedrally oriented bonds. They account for about 80% of the bonds in each snapshot. Thus, these bonds form the basis or framework of the hydrogen bond network of water. The other, improper bonds have a substantially shorter lifetime; these are weak, bifurcated, and quickly switching bonds.     

Hydrogen bond and residence dynamics of ion-water and water-water pairs in supercritical aqueous ionic solutions: dependence on ion size and density

We have carried out a series of molecular dynamics simulations to investigate the hydrogen bond and residence dynamics of X(-)-water (X=F, Cl, and I) and pairs in aqueous solutions at a temperature of 673 K. The calculations are done at six different water densities ranging from 1.0 to 0.15 g cm(-3). The hydrogen bonds are defined by using a set of configurational criteria with respect to the anion(oxygen)-oxygen and anion(oxygen)-hydrogen distances and the anion(oxygen)-oxygen-hydrogen angle for an anion(water)-water pair. The F(-)-water hydrogen bonds are found to have a longer lifetime than all other hydrogen bonds considered in the present study. The lifetime of Cl(-)-water hydrogen bonds is shorter than that of F(-)-water hydrogen bonds but longer than the lifetime of water-water hydrogen bonds. The lifetimes of I(-)-water and water-water hydrogen bonds are found to be very similar. Generally, the lifetimes of both anion-water and water-water hydrogen bonds are found to be significantly shorter than those found under ambient conditions. In addition to hydrogen bond lifetimes, we have also calculated the residence times and the orientational relaxation times of water molecules in ion(water) hydration shells and have discussed the correlations of these dynamical quantities with the observed dynamics of anion(water)-water hydrogen bonds as functions of the ion size and density of the supercritical solutions.     

Computer simulation of the hydrogen bond lifetime and the mechanism of the structural rearrangement of water

The concept of a hydrogen bond lifetime is analyzed in a computer experiment. It is shown that different definitions of the lifetime of a hydrogen bond characterize definite stages in the microdynamics of a liquid. The lifetimes of hydrogen bonds are calculated for water using the TIP4P and TIP4B-HB model potentials. A number of features in the mechanism of the structural rearrangement of the nearest surrounding is determined by comparing them.     

The effect of external forces on the initial dissociation of RDX (1,3,5‐trinitro‐1,3,5‐triazine): A mechanochemical study

Experimental and theoretical studies have proposed different initiation reactions for the decomposition of hexahydro‐1,3,5‐trinitro‐1,3,5‐triazine (RDX). Three primary reactions are considered to start RDX decomposition: homolytic N? N bond fission, HONO elimination, and concerted fission of C? N bonds. The focus of this article is to study the effect of external forces on the energy barrier and reaction energies of all three mechanisms. We used the Nudged Elastic Band method along with ab initio Density Functional Theory within the framework of a generalized force‐modified potential energy surface (G‐FMPES) to calculate the minimum energy paths at different compressive (corresponding to pressure between approximately 6 and 294 MPa) and expansive force values (between 10 and 264 pN). For all three reactions, the application of an expansive force increases the exothermicity and lowers the energy barriers to different extents, while a compressive force decreases the exothermicity and raises the energy barrier to different extents.     

Dynamic strength of molecularly bonded surfaces

This study reports a theoretical analysis of the forced separation of two adhesive surfaces linked via a large number of parallel noncovalent bonds. To describe the bond kinetics, we implement a three-state reaction model with kinetic rates obtained from a simple integral expression of the mean first passage time for diffusive barrier crossing in a pulled-distance-dependent potential. We then compute the rupture force for the separation of adhesive surfaces at a constant rate. The results correspond well with a Brownian dynamics simulation of the same system. The separation rate relative to the intrinsic relaxation time of the bonds defines three loading regimes and the general dependence of the adhesion on kinetic or thermodynamic parameters of the bonds. In the equilibrium regime, the rupture force asymptotically approaches the equilibrium rupture force, which increases linearly with the equilibrium bond energy. In the near-equilibrium regime, the rupture force increases with the separation rate and increasingly correlates with the bond rupture barrier. In the far-from-equilibrium regime where rebinding is irrelevant, the rupture force varies linearly with the rupture barrier.     

Dispersion and Hydrogen Bonding Rule: Why the Vaporization Enthalpies of Aprotic Ionic Liquids Are Significantly Larger than those of Protic Ionic liquids

It is well known that gas‐phase experiments and computational methods point to the dominance of dispersion forces in the molecular association of hydrocarbons. Estimates or even quantification of these weak forces are complicated due to solvent effects in solution. The dissection of interaction energies and quantification of dispersion interactions is particularly challenging for polar systems such as ionic liquids (ILs) which are characterized by a subtle balance between Coulomb interactions, hydrogen bonding, and dispersion forces. Here, we have used vaporization enthalpies, far‐infrared spectroscopy, and dispersion‐corrected calculations to dissect the interaction energies between cations and anions in aprotic (AILs), and protic (PILs) ionic liquids. It was found that the higher total interaction energy in PILs results from the strong and directional hydrogen bonds between cation and anion, whereas the larger vaporization enthalpies of AILs clearly arise from increasing dispersion forces between ion pairs.     

Nonradiative decay dynamics of methyl-4-hydroxycinnamate and its hydrated complex revealed by picosecond pump-probe spectroscopy

The lifetimes of methyl 4-hydroxycinnamate (OMpCA) and its mono-hydrated complex (OMpCA-H(2)O) in the S(1) state have been measured by picosecond pump-probe spectroscopy in a supersonic beam. For OMpCA, the lifetime of the S(1)-S(0) origin is 8-9 ps. On the other hand, the lifetime of the OMpCA-H(2)O complex at the origin is 930 ps, which is ～100 times longer than that of OMpCA. Furthermore, in the complex the S(1) lifetime shows rapid decrease at an energy of ～200 cm(-1) above the origin and finally becomes as short as 9 ps at ～500 cm(-1). Theoretical calculations with a symmetry-adapted cluster-configuration interaction (SAC-CI) method suggest that the observed lifetime behavior of the two species is described by nonradiative decay dynamics involving trans → cis isomerization. That is both OMpCA and OMpCA-H(2)O in the S(1) state decay due to the trans → cis isomerization, and the large difference of the lifetimes between them is due to the difference of the isomerization potential energy curve. In OMpCA, the trans → cis isomerization occurs smoothly without a barrier on the S(1) surface, while in the OMpCA-H(2)O complex, there exists a barrier along the isomerization coordinate. The calculated barrier height of OMpCA-H(2)O is in good agreement with that observed experimentally.     

Why are the Homoleptic Diyl Complexes M(InR)4 with M = Ni and Pt Stable Compounds while only Ni(CO)4 but not Pt(CO)4 can become Isolated? A Theoretical Study of M(EMe)44 and M(CO)4 (M = Ni,Pd, Pt; E = B,Al, Ga,In, Tl)

The equilibrium geometries and first bond dissociation energies of the homoleptic complexes M(EMe)₄ and M(CO)₄ with M = Ni, Pd, Pt and E = B, Al, Ga, In, Tl have been calculated at the gradient corrected DFT level using the BP86 functionals. The electronic structure of the metal‐ligand bonds has been examined with the topologial analysis of the electron density distribution. The nature of the bonding is revealed by partitioning the metal‐ligand interaction energies into contributions by electrostatic attraction, covalent bonding and Pauli repulsion. The calculated data show that the M‐CO and M‐EMe bonding is very similar. However, the M‐EMe bonds of the lighter elements E are much stronger than the M‐CO bonds. The bond energies of the latter are as low or even lower than the M‐TlMe bonds. The main reason why Pd(CO)₄ and Pt(CO)₄ are unstable at room temperature in a condensed phase can be traced back to the already rather weak bond energy of the Ni‐CO bond. The Pd‐L bond energies of the complexes with L = CO and L = EMe are always 10 — 20 kcal/mol lower than the Ni‐L bond energies. The calculated bond energy of Ni(CO)₄ is only D_o = 27 kcal/mol. Thus, the bond energy of Pd(CO)₄ is only D_o = 12 kcal/mol. The first bond dissociation energy of Pt(CO)₄ is low because the relaxation energy of the Pt(CO)₃ fragment is rather high. The low bond energies of the M‐CO bonds are mainly caused by the relatively weak electrostatic attraction and by the comparatively large Pauli repulsion. The σ and π contributions to the covalent M‐CO interactions have about the same strength. The π bonding in the M‐EMe bonds is less than in the M‐CO bonds but it remains an important part of the bond energy. The trends of the electrostatic and covalent contributions to the bond energies and the σ and π bonding in the metal‐ligand bonds are discussed.     

An anchor-dependent molecular docking process for docking small flexible molecules into rigid protein receptors

A molecular docking method designated as ADDock, anchor- dependent molecular docking process for docking small flexible molecules into rigid protein receptors, is presented in this article. ADDock makes the bond connection lists for atoms based on anchors chosen for building molecular structures for docking small flexible molecules or ligands into rigid active sites of protein receptors. ADDock employs an extended version of piecewise linear potential for scoring the docked structures. Since no translational motion for small molecules is implemented during the docking process, ADDock searches the best docking result by systematically changing the anchors chosen, which are usually the single-edge connected nodes or terminal hydrogen atoms of ligands. ADDock takes intact ligand structures generated during the docking process for computing the docked scores; therefore, no energy minimization is required in the evaluation phase of docking. The docking accuracy by ADDock for 92 receptor-ligand complexes docked is 91.3%. All these complexes have been docked by other groups using other docking methods. The receptor-ligand steric interaction energies computed by ADDock for some sets of active and inactive compounds selected and docked into the same receptor active sites are apparently separated. These results show that based on the steric interaction energies computed between the docked structures and receptor active sites, ADDock is able to separate active from inactive compounds for both being docked into the same receptor.