Measured Dissociation Rate Research Articles

CO2-TBAB semi-clathrate hydrate dissociation behaviour in individual capsules: A new two-stage numerical model and parametric study

Gas hydrates have a wide implementation in the capture, storage, transport and utilisation of a range of gases, in which the dissociation kinetics is of great importance to gas transport and recovery efficiency. Encapsulation has been proven an effective technique to enhance gas–liquid mass transfer and thus improve gas hydrate formation kinetics. However, the dissociation behaviour of gas hydrate in individual capsules remains unknown. In this work, the dissociation kinetics of encapsulated CO2-TBAB semi-clathrate hydrates in different shapes are experimentally investigated under various operating conditions, and, for the first time, a two-stage numerical model is developed which integrates mass transfer, heat transfer and the intrinsic gas hydrate reaction kinetics to simulate the gas hydrate dissociation process. The effects of temperature, pressure, capsule volume and capsule geometry on gas hydrate dissociation kinetics are investigated. The results reveal that the proposed model is capable of capturing two distinct experimentally-observed dissociation stages, a rapid and subsequently slow stage according to the measured dissociation rate. Surface-to-volume ratio of the capsule and the dissociation driving force are the two main factors influencing the dissociation kinetics. The ring-shaped capsule exhibits the most efficient dissociation process due to its high surface-to-volume ratio and long transition time to the slow dissociation stage. This work enhances the understanding of gas hydrate dissociation behaviour in individual capsules and guides the manipulation of dissociation for efficient hydrate-based gas transport and recovery.

Nonequilibrium Dissociation and Recombination Models for Hypersonic Flows

A recombination reaction model for high-temperature chemical kinetics is analytically derived from ab initio simulation data. When atoms recombine, the kinetic rate model shows that product molecules favor high vibrational energy states. In this manner, recombination repopulates high vibrational energy states depleted by dissociation, in a high-temperature reacting gas. Coupling of internal energy relaxation, dissociation, and recombination results in depleted or overpopulated (relative to a corresponding Boltzmann distribution) vibrational energy distributions. Through a simple model, we show that non-Boltzmann behavior, in other words, depletion or overpopulation of high-energy states, is not only linked to thermal nonequilibrium but also chemical nonequilibrium. The mathematical derivation also indicates that the conventional approach for modeling recombination rates, where shock-tube dissociation rate measurements are combined with the principle of detailed balance, is incorrect. The complete analytical dissociation/recombination model embeds all relevant kinetic processes, including specific terms for translation/rotation/vibration/chemistry coupling, anharmonic and quasi-bound effects, and non-Boltzmann depletion and overpopulation effects. The model is a multitemperature model that can be used within computational fluid dynamics simulations with no appreciable increase in computational expense. Finally, because the model is analytical, containing separate terms for various physical effects, further model simplification could be performed depending on the flow conditions of interest.

High-Throughput Single-Cell TCR-pMHC Dissociation Rate Measurements Performed by an Autonomous Microfluidic Cellular Processing Unit.

We developed an integrated microfluidic cellular processing unit (mCPU) capable of autonomously isolating single cells and performing measurements and on-the-fly analysis of cell-surface dissociation rates, followed by recovery of selected cells. We performed proof-of-concept, high-throughput single-cell experiments characterizing pMHC-TCR interactions on live CD8+ T cells. The mCPU platform analyzed TCR-pMHC dissociation rates with a throughput of 50 cells per hour and hundreds of cells per run, and we demonstrate that cells can be selected, enriched, and easily recovered from the device.

Calculation of strong‐collision dissociation rate constants from NASA thermodynamic polynomials

AbstractA new method for calculating low‐pressure strong‐collision rate constants of dissociation and recombination reactions was proposed. The method is based on determining the density of states of the internal degrees of freedom of the reactant molecule by applying the inverse Laplace transform to the respective partition function, which, in turn, is calculated from the thermodynamic properties in the form of NASA polynomials. The proposed model is universal in the sense that the required NASA polynomials can be calculated using molecular properties obtained by various methods, both theoretical and experimental or a combination thereof. In the present study, the NASA polynomials were taken from the available databases or calculated from thermodynamic functions, either tabulated or determined by statistical mechanics in the rigid‐rotor harmonic‐oscillator approximation, with a simple anharmonicity correction introduced when necessary. In addition, a model for calculating the rotational factor is developed and tested. It is based on determination of the centrifugal barrier as a function of the dissociating bond length at a given rotational energy through calculating the principal moments of inertia of the molecule at each step of elongation of the bond. The proposed approach is exemplified for the dissociation of the H2O, HO2, and H2O2 molecules and the corresponding reverse reactions. A comparison with the available experimental data made it possible to estimate the weak‐collision efficiency. At high temperatures, for all the reactions studied, the weak collision efficiency appears to be quite reasonable, whereas, at low temperatures, the situation is unsatisfactory, except perhaps for H2O dissociation. Given that the energy threshold E0 of dissociation reactions is typically well known, the calculated and measured dissociation rate constants are represented and handled in terms of the preexponential factor A(T) in the expression k(T) = A(T)exp(−E0/RT). A new formula for fitting A(T) was proposed: log A(T) = a + b(1000/T) + c(1000/T)p, which turned out to be a good approximation for the preexponential factors of not only the rate constants but also the equilibrium constants.

Direct observation of individual tubulin dimers binding to growing microtubules

The biochemical basis of microtubule growth has remained elusive for over 30 years despite being fundamental for both cell division and associated chemotherapy strategies. Here, we combine interferometric scattering microscopy with recombinant tubulin to monitor individual tubulins binding to and dissociating from growing microtubule tips. We make direct, single-molecule measurements of tubulin association and dissociation rates. We detect two populations of transient dwell times and determine via binding-interface mutants that they are distinguished by the formation of one interprotofilament bond. Applying a computational model, we find that slow association kinetics with strong interactions along protofilaments best recapitulate our data and, furthermore, predicts plus-end tapering. Overall, we provide the most direct and complete experimental quantification of how microtubules grow to date.

Direct Observation of Individual Tubulin Dimers Binding to Growing Microtubules

The biochemical basis of microtubule growth has remained elusive for over 30 years despite being fundamental for both cell division and associated chemotherapy strategies. Here, we combine interferometric scattering microscopy with recombinant tubulin to monitor individual tubulins binding to and dissociating from growing microtubule tips. We make direct, single-molecule measurements of tubulin association and dissociation rates. We detect two populations of transient dwell times and determine via binding-interface mutants that they are distinguished by the formation of one interprotofilament bond. Applying a computational model, we find that slow association kinetics with strong interactions along protofilaments best recapitulate our data and, furthermore, predicts plus-end tapering. Overall, we provide the most direct and complete experimental quantification of how microtubules grow to date.

Kinetics of Transient Protein Complexes Determined via Diffusion-Independent Microfluidic Mixing and Fluorescence Stoichiometry.

Low-affinity protein complexes and their transient states are difficult to measure in single-molecule experiments because of their low population at low concentrations. A prominent solution to this problem is the use of microfluidic mixing devices, which rely on diffusion-based mixing. This is not ideal for multiprotein complexes, as the single-molecule fluorescence signal is dominated by the already dissociated species. Here, we designed a microfluidic device with mixing structures for fast and homogeneous mixing of components with varying diffusion coefficients and for fluorescence measurements at a defined single-molecule concentration. This enables direct measurement of dissociation rates at a broad range of timescales from a few milliseconds to several minutes. This further allows us to measure structural properties and stoichiometries of protein complexes with large equilibrium dissociation constants ( KD's) of 5 μM and above. We used the platform to measure structural properties and dissociation rates of heat shock protein 90 (Hsp90) dimers and found at least two dissociation rates which depend on the nucleotide state. Finally, we demonstrate the capability for measuring also equilibrium dissociation constants, resulting in the determination of both the kinetics and thermodynamics of the system under investigation.

Selective Covalent Chemistry via Gas-Phase Ion/ion Reactions: An Exploration of the Energy Surfaces Associated with N-Hydroxysuccinimide Ester Reagents and Primary Amines and Guanidine Groups.

Selective covalent bond forming reactions (referred to as covalent reactions) can occur in gas-phase ion/ion reactions and take place via the formation of a long-lived chemical complex. The gas-phase ion/ion reactivity between sulfo-N-hydroxysuccinimide (sulfo-NHS) ester reagent anions and peptide cations containing a primary amine or guanidine group has been examined via DFT calculations and complex dissociation rate measurements. The results reveal insights regarding the roles of the barriers of competing processes within the complex. When the covalent reaction is exothermic, two prototypical cases, determined by the nature of the energy surface, are apparent. The product partitioning between covalent reaction and simple proton transfer upon dissociation of the long-lived complex is sensitive to activation conditions when the transition state barrier for covalent reaction is relatively high (case 1) but is insensitive to activation conditions when the transition state barrier is relatively low (case 2). Covalent reaction efficiencies are very high in case 2 scenarios, such as when the reactive site is a guanidine and the anion attachment site is a guanidinium ion. Covalent reaction efficiencies are variable, and generally low, in case 1 scenarios, such as when an amine is the reactive site and an ammonium ion is the site of anion attachment. A relatively long slow-heating step prior to the complex dissociation step, however, can dramatically increase covalent reaction yield in case 1 scenarios. Graphical Abstract ᅟ.

Nucleotides Linkage Analysis of RecBCD DNA Helicase

RecBCD is a bacterial enzyme complex that possesses both DNA helicase and nuclease activities necessary for its biological function. RecBCD is both a continuous and a processive DNA helicase, with an unwinding rate of ∼ 1,600 bp/s. Research on RecBCD function and mechanism in last decades had provided wealth of information on its biochemistry, structure and unwinding mechanism. Still, very little is known about the biochemical transitions, and the nucleotide linkage between RecBCD and DNA during its ATPase cycle. In this work we present thermodynamic linkage analysis using multiple approaches of different nucleotides states of RecBCD free and bound to ssDNA or dsDNA. Primarily, we have purified RecBCD, free of nucleic acids contaminates, which limits such measurements. We show that a nucleotide state mimicking ATP hydrolysis binds with the tightest affinity in comparison to the ADP or nucleotide free binding states in the presence of either ssDNA or dsDNA. Furthermore, by utilizing transient kinetics approach, we have measured dissociation rate constants of ssDNA and dsDNA from RecBCD with different nucleotides states. We demonstrate that ADP state increases the dissociation rate constant of ssDNA in comparison to all these states: dsDNA-bound, nucleotide free or with the binding of ATP states. Collectively, our results identified a strong nucleotide binding state of the RecBCD complex and a second nucleotide state, which is most likely to dissociate from the DNA track during the course of unwinding and translocation reaction. These results will allow us to construct a model of the different biochemical intermediates during a single ATPase cycle and reveal the allostery that may exist between RecBCD subunits during its unwinding reaction.

Fluorescently Labeled Tarantula Toxin Reveals Voltage Dependent Adhesion to K+ Channels

Among the most potent allosteric modulators of voltage-gated potassium channels are peptide toxins from arachnids. Guangxitoxin-1E is an exemplar of this class of ligands, having effects at nanomolar concentrations and shifting gating of Kv2.1 to a positive voltage range, beyond physiological potentials. We have synthesized biologically active variants of this toxin with unique chemically reactive groups that allow conjugation to probes that allow visualization of toxin adherence to channels on living cells. The association of toxin with Kv2.1 channels was found to be strongly voltage dependent, having different affinities for resting and activated states of voltage sensors. To compose structural hypotheses for the toxin-channel interactions that underlie allosteric effector properties, we built structural models of the toxin-channel interaction using the Rosetta-Membrane homology method and the Kv1.2-2.1 coordinates as template, to create models of Kv2.1 voltage sensing domains. Conformations of activated and resting states were generated following a sliding helix model. The toxin was then docked to these multiple voltage sensor conformations using the Rosetta Dock method to identify low energy complexes. Experimentally, measurement of toxin association and dissociation rates by voltage clamp and with fluorescently labeled toxins create constraints that define its mechanism of action. The differential adherence of toxin to resting and activated voltage sensor conformations drives allosteric modulation of channels. By measuring gating state-dependent affinities, this methodology creates a new means of assessing the potency and action of allosteric ion channel modulators. In combination with computational structure prediction and design this strategy could lead to development of voltage sensor modulators with novel state-dependence.

Spastin's Microtubule-Binding Properties and Comparison to Katanin

Spastin and katanin are ring-shaped hexameric AAA ATPases that sever microtubules, and thus crucially depend on a physical interaction with microtubules. For the first time, we report here the microtubule binding properties of spastin at the single-molecule level, and compare them to katanin. Microscopic fluorescence assays showed that human spastin bound to microtubules by ionic interactions, and diffused along microtubules with a diffusion coefficient comparable to katanin. The microscopic measurement of landing and dissociation rates demonstrated the ionic character of the interaction, which could be mapped to a patch of three lysine residues outside of the catalytic domain of human spastin. This motif is not conserved in Drosophila spastin or katanin, which also bound by non-catalytic parts of the protein. The binding affinities of spastin and katanin were nucleotide-sensitive, with the lowest affinities under ADP,, the highest under ATP-γS conditions. These changes correlated with the formation of higher oligomeric states, as shown in biochemical experiments and electron microscopic images. Vice versa, the artificial dimerization of human spastin by addition of a coiled coil led to a constitutively active enzyme. These observations suggest that dimer formation is a crucial step in the formation of the active complex, and thus the severing process by spastin.

Single-Molecule Measurements of Dissociation Rates and Energy Landscapes of Binary trans SNARE Complexes in Parallel versus Antiparallel Orientation

Interactions between synaptobrevin 2 (Sb2) and syntaxin 1A (Sx1A) can be readily isolated and studied with the use of force spectroscopy single-molecule measurements. We studied interactions between Sx1A and Sb2 in two different orientations (parallel and antiparallel) using four different terminus configurations of these proteins. Force-loading experiments indicated that protein pairs in any configuration/orientation are zippered. We measured the extension and force for disassembly of these interactions, calculated the spontaneous dissociation lifetimes, and determined their free energies, enthalpies, and entropies. Although the free energies were very similar for all four configurations (∼28 kBT (Eyring model) and ∼20 kBT (Kramers model)), the enthalpy changes of binary Sx1A-Sb2 interactions varied between 24.7 kBT and 33.1 kBT. This variation is consistent with the conformation changes that occur during disassembly of the various protein terminus configurations, as verified by alterations in the extension. The parallel interactions appear to be energetically somewhat advantageous over antiparallel configurations/orientation, especially when the N-termini of Sx1A-Sb2 are left to interact freely.

Analysis of the Binding Forces Driving the Tight Interactions between β-Lactamase Inhibitory Protein-II (BLIP-II) and Class A β-Lactamases

β-Lactamases hydrolyze β-lactam antibiotics to provide drug resistance to bacteria. β-Lactamase inhibitory protein-II (BLIP-II) is a potent proteinaceous inhibitor that exhibits low picomolar affinity for class A β-lactamases. This study examines the driving forces for binding between BLIP-II and β-lactamases using a combination of presteady state kinetics, isothermal titration calorimetry, and x-ray crystallography. The measured dissociation rate constants for BLIP-II and various β-lactamases ranged from 10(-4) to 10(-7) s(-1) and are comparable with those found in some of the tightest known protein-protein interactions. The crystal structures of BLIP-II alone and in complex with Bacillus anthracis Bla1 β-lactamase revealed no significant side-chain movement in BLIP-II in the complex versus the monomer. The structural rigidity of BLIP-II minimizes the loss of the entropy upon complex formation and, as indicated by thermodynamics experiments, may be a key determinant of the observed potent inhibition of β-lactamases.

Direct measurement of formation and dissociation rate and storage capacity of dry water methane hydrates

Dry water (DW) has been recently demonstrated to be an effective medium for methane storage in a hydrated form. Here, a series of experiments have been carried out on dry water methane hydrates (DW–MH) to investigate their formation and dissociation rates, storage capacity and structural characteristics. The result shows that the storage capacity of MH increases at least 10% by using DW relative to using surfactants like sodium dodecyl sulfate (SDS) solution. Also, it is found that controls on pressure–temperature (P–T) condition have influences on the induction and reaction time of DW–MH formation, i. e. the induction and reaction time are much shorter when the reaction cell is cooled to ~ 3 °C first. On the basis of Raman spectra, the hydration number is calculated as 5.934 ± 0.06 at different positions of the DW–MH, which suggests that the sample is very homogeneous. The dissociation process of the DW–MH sample exhibits a rapid release of methane gas at the first stage of dissociation. Although hydrate dissociation is prevented by the effect of self preservation, most methane gas has released from the hydrate, however, before the self preservation occur.

Shock Tube and Theoretical Studies on the Thermal Decomposition of Propane: Evidence for a Roaming Radical Channel

The thermal decomposition of propane has been studied using both shock tube experiments and ab initio transition state theory-based master equation calculations. Dissociation rate constants for propane have been measured at high temperatures behind reflected shock waves using high-sensitivity H-ARAS detection and CH(3) optical absorption. The two major dissociation channels at high temperature are C(3)H(8) → CH(3) + C(2)H(5) (eq 1a) and C(3)H(8) → CH(4) + C(2)H(4) (eq 1b). Ultra high-sensitivity ARAS detection of H-atoms produced from the decomposition of the product, C(2)H(5), in (1a), allowed measurements of both the total decomposition rate constants, k(total), and the branching to radical products, k(1a)/k(total). Theoretical analyses indicate that the molecular products are formed exclusively through the roaming radical mechanism and that radical products are formed exclusively through channel 1a. The experiments were performed over the temperature range 1417-1819 K and gave a minor contribution of (10 ± 8%) due to roaming. A multipass CH(3) absorption diagnostic using a Zn resonance lamp was also developed and characterized in this work using the thermal decomposition of CH(3)I as a reference reaction. The measured rate constants for CH(3)I decomposition agreed with earlier determinations from this laboratory that were based on I-atom ARAS measurements. This CH(3) diagnostic was then used to detect radicals from channel 1a allowing lower temperature (1202-1543 K) measurements of k(1a) to be determined. Variable reaction coordinate-transition state theory was used to predict the high pressure limits for channel (1a) and other bond fission reactions in C(3)H(8). Conventional transition state theory calculations were also used to estimate rate constants for other tight transition state processes. These calculations predict a negligible contribution (<1%) from all other bond fission and tight transition state processes, indicating that the bond fission channel (1a) and the roaming channel (1b) are indeed the only active channels at the temperature and pressure ranges of the present experiments. The predicted reaction exo- and endothermicities are in excellent agreement with the current version of the Active Thermochemical Tables. Master equation calculations incorporating these transition state theory results yield predictions for the temperature and pressure dependence of the dissociation rate constants for channel 1a. The final theoretical results reliably reproduce the measured dissociation rate constants that are reported here and in the literature. The experimental data are well reproduced over the 500-2500 K and 1 × 10(-4) to 100 bar range (errors of ∼15% or less) by the following Troe parameters for Ar as the bath gas: k(∞) = 1.55 × 10(24)T(-2.034) exp(-45 490/T) s(-1), k(0) = 7.92 × 10(53)T(-16.67) exp(-50 380/T) cm(3) s(-1), and F(c) = 0.190 exp(-T/3091) + 0.810 exp(-T/128) + exp(-8829/T).

A Computational and Experimental Approach To Investigate Bepridil Binding with Cardiac Troponin

Cardiac troponin is a Ca(2+)-dependent switch for the contraction in heart muscle and a potential target for drugs in the therapy of heart failure. Bepridil is a drug that binds to troponin and increases calcium sensitivity of muscle contraction. Because bepridil has been well studied, it is a good model for analysis by computational and experimental methods. Molecular dynamics (MD) simulations were performed on troponin complexes of different sizes in the presence and absence of bepridil bound within the hydrophobic pocket at the N-terminal domain of troponin C. About 100 ns of simulation trajectory data were generated, which were analyzed using cross-correlation analyses and MMPBSA and MMGBSA techniques. The results indicated that bepridil binding within the hydrophobic pocket of cardiac TnC decreases the interaction of TnC with TnI at both the N-domain of TnC and the C-domain of TnC, and decreases the correlations of motions among the segments of the troponin subunits. The estimated calcium-binding affinities using MMPBSA showed that bepridil has a sensitizing effect for the isolated system of TnC, but loses this effect for the complex. Our experimental measurements of calcium dissociation rates were consistent with that prediction. We also observed that while bepridil enhanced the troponin-tropomyosin-actin-activated ATPase activity of myosin S1 at low calcium concentrations it was slightly inhibitory at high calcium concentrations. Bepridil increases the ATPase activity and force generation in muscle fibers, but its effects appear to depend on the concentration of calcium.

Phosphodiesterases Catalyze Hydrolysis of cAMP-bound to Regulatory Subunit of Protein Kinase A and Mediate Signal Termination

Although extensive structural and biochemical studies have provided molecular insights into the mechanism of cAMP-dependent activation of protein kinase A (PKA), little is known about signal termination and the role of phosphodiesterases (PDEs) in regulatory feedback. In this study we describe a novel mode of protein kinase A-anchoring protein (AKAP)-independent feedback regulation between a specific PDE, RegA and the PKA regulatory (RIα) subunit, where RIα functions as an activator of PDE catalysis. Our results indicate that RegA, in addition to its well-known role as a PDE for bulk cAMP in solution, is also capable of hydrolyzing cAMP-bound to RIα. Furthermore our results indicate that binding of RIα activates PDE catalysis several fold demonstrating a dual function of RIα, both as an inhibitor of the PKA catalytic (C) subunit and as an activator for PDEs. Deletion mutagenesis has localized the sites of interaction to one of the cAMP-binding domains of RIα and the catalytic PDE domain of RegA whereas amide hydrogen/deuterium exchange mass spectrometry has revealed that the cAMP-binding site (phosphate binding cassette) along with proximal regions important for relaying allosteric changes mediated by cAMP, are important for interactions with the PDE catalytic domain of RegA. These sites of interactions together with measurements of cAMP dissociation rates demonstrate that binding of RegA facilitates dissociation of cAMP followed by hydrolysis of the released cAMP to 5'AMP. cAMP-free RIα generated as an end product remains bound to RegA. The PKA C-subunit then displaces RegA and reassociates with cAMP-free RIα to regenerate the inactive PKA holoenzyme thereby completing the termination step of cAMP signaling. These results reveal a novel mode of regulatory feedback between PDEs and RIα that has important consequences for PKA regulation and cAMP signal termination.

Modeling the Unbinding Mechanism of the Neutral and Anionic Semi-Quinone from the QA Site of Bacterial Reaction Centers Using Steered Molecular Dynamics Simulations

Bacterial photosynthetic reactions centers are large integral membrane proteins that carry out a series of light initiated electron transfer reactions between bound co-factors. In the QA binding site ubiquinone is singly reduced to the anionic semi-quinone. Previous experimental studies using hydroxyl quinones at a pH above the pKa, showed that neutral and anionic quinone species have similar affinity for the QA site (Madeo et. al Biochemistry, 2005, 44 10994-11004). Despite this, anionic quinones dissociate from the QA site 10⊥3 times more slowly than neutral quinones. This suggests that there are large kinetic barriers created by the protein for the dissociation of anionic quinones that are not present in the neutral state. The present study further investigates these barriers by applying constant-velocity steered molecular dynamics (SMD) to compare the unbinding of the neutral native ubiquinone and its anionic semiquinone. The same starting structure (1aij.pdb) is used in ubiquinone and semiquinone simulations, with partial charges adjusted to represent the equilibrated residue charge states. All simulations were performed with the GROMACS package with the OPLS-AA force field. A structural analysis of the trajectories generated during the unbinding of quinones identifies residues of the protein making stronger interactions with semiquinone than with ubiquinone and thus possibly contributing to the kinetic barriers. The magnitude of the energetic barrier is compared to the measured dissociation rate of anionic hydroxyl quinones. Supported by NSF-MCB-1022208.

Microfluidic Measurement of Antibody−Antigen Binding Kinetics from Low-Abundance Samples and Single Cells

We present a simple microfluidic fluorescence bead assay for accurately measuring antibody-antigen binding kinetics with a standard inverted fluorescent microscope. We measured association and dissociation rate constants from antibody-antigen interactions spanning nearly 4 orders of magnitude in equilibrium binding affinity (30 pM-100 nM). Two versions of this assay are presented, which allow for dissociation rate measurements either directly, by use of fluorescently labeled antigen, or indirectly, by use of unlabeled antigen. We also demonstrate simultaneous, multiplexed binding measurements of multiple antibody-antigen interactions using a combination of spectral separation and spatial localization. Complete antibody-antigen binding kinetics were measured for as little as 8 × 10⁴ antibody molecules (~132 zeptomoles) immobilized on a single bead and less than 2 × 10⁶ antibodies (~3 attomoles) loaded into the microfluidic device, a reduction in detection limit and sample consumption of 4 orders of magnitude when compared to surface plasmon resonance (SPR) spectroscopy and alternative measurement techniques. We show that the microfluidic bead assay, when combined with small volume compartmentalization, enables direct measurement of antigen binding kinetics of antibodies secreted from single hybridoma cells. We anticipate that this assay will be useful as a routine analytical tool for studying molecular interactions as well as for screening primary antibody-secreting plasma cells isolated from immunized animals.

Diffusion of the Restriction Nuclease EcoRI along DNA

Many specific sequence DNA binding proteins locate their target sequence by first binding to DNA nonspecifically, then by linearly diffusing or hopping along DNA until either the protein dissociates from the DNA or it finds the recognition sequence. We have devised a method for measuring one-dimensional diffusion along DNA based on the ratio of the dissociation rate of protein from DNA fragments containing one specific binding site to the dissociation rate from DNA fragments containing two specific binding sites. Our extensive measurements of dissociation rates and specific–nonspecific relative binding constants of the restriction nuclease EcoRI enable us to determine the diffusion rate of nonspecifically bound protein along the DNA. By varying the distance between the two binding sites, we confirm a linear diffusion mechanism. The sliding rate is relatively insensitive to salt concentration and osmotic pressure, indicating that the protein moves smoothly along the DNA probably following the helical phosphate-sugar backbone of DNA. We calculate a diffusion coefficient for EcoRI of 3 × 10 4 bp 2 s − 1 EcoRI is able to diffuse ∼ 150 bp, on average, along the DNA in 1 s. This diffusion rate is about 2000-fold slower than the diffusion of free protein in solution. A factor of 40–50 can be accounted for by rotational friction resulting from following the helical path of the DNA backbone. Two possibilities could account for the remaining activation energy: salt bridges between the DNA and the protein are transiently broken, or the water structure at the protein–DNA interface is disrupted as the two surfaces move past each other.