Hammer, Daniel A
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Publication Competitive Hybridization Kinetics Reveals Unexpected Behavior Patterns(2005-11-01) Hammer, Daniel A; Zhang, Ying; Graves, David JAlthough the kinetics of hybridization between a soluble polynucleotide and an immobilized complementary sequence have been studied by others, it is almost universally assumed that the interaction between each probe/target pair can be treated as a separate event. This simplifies the mathematics considerably, but it can give a false picture of the extent of hybridization that one achieves at equilibrium as well as the relative quantities of each hybridized pair during the approach to equilibrium. Here we solve the relevant kinetics equations simultaneously using Mathematica as a simulation language. Among the interesting results of this study are that, for certain circumstances, the relative ratio of incorrect to correct hybrids can change dramatically with time; that the relative abundances of two pairs are not what one would expect based on their equilibrium dissociation constants; that the volume of a wash solution after hybridization can have a large effect on results; and the fact that a short wash is typically better than a long one. We show that an optimum wash time exists for a given set of conditions. In addition, the ratio of soluble to insoluble (spotted) molecules can influence results substantially. Finally, the true levels of rare transcripts can be masked by the presence of highly abundant ones. Code is supplied to enable others to study conditions beyond those presented in this article.Publication Tyrosine Sulfation Enhances but Is Not Required for PSGL-1 Rolling Adhesion on P-Selectin(2001-10-01) Rodgers, Stephen D; Camphausen, Raymond T; Hammer, Daniel AP-selectin glycoprotein ligand-1 (PSGL-1) is a large (240 kDa) glycoprotein found on the surface of nearly all leukocytes. The mature molecule is decorated with multiple N- and O-linked glycans and displays copies of the tetrasaccharide sialyl-Lewisx (sLeX), as well as a cluster of three tyrosine sulfate (tyr-SO3) groups near the N-terminus of the processed protein. Previous studies have suggested that PSGL-1 needs to be tyrosine-sulfated, in addition to glycosylated with sLeX, to successfully interact with P-selectin. To better understand how biochemical features of the PSGL-1 ligand are related to its adhesion phenotype, we have measured the dynamics of adhesion under flow of a series of well-defined PSGL-1 variants that differ in their biochemical modification, to both P- and E-selectin-coated substrates. These variants are distinct PSGL-1 peptides: one that possesses sLeX in conjunction with three N-terminal tyr-SO3 groups (SGP3), one that possesses sLeX without tyrosine sulfation (GP1), and one that lacks sLeX but has three N-terminal tyr-SO3 groups (SP3). Although all peptides expressing sLeX, tyr-SO3, or both supported some form of rolling adhesion on P-selectin, only peptides expressing sLeX groups showed rolling adhesion on E-selectin. On P-selectin, the PSGL-1 peptides demonstrated a decreasing strength of adhesion in the following order: SGP3 > GP1 > SP3. Robust, rolling adhesion on P-selectin was mediated by the GP1 peptide, despite its lack of tyrosine sulfation. However, the addition of tyrosine sulfation to glycosylated peptides (SGP3) creates a super ligand for P-selectin that supports slower rolling adhesion at all shear rates and supports rolling adhesion at much higher shear rates. Tyrosine sulfation has no similar effect on PSGL-1 rolling on E-selectin. Such functional distinctions in rolling dynamics are uniquely realized with a cell-free system, which permits precise, unambiguous identification of the functional activity of adhesive ligands. These findings are consistent with structural and functional characterizations of the interactions between these peptides and E- and P-selectin published recently.Publication Pore Stability and Dynamics in Polymer Membranes(2003-11-15) Bermudez, Harry; Hammer, Daniel A; Aranda-Espinoza, Helim; Discher, Dennis EVesicles self-assembled from amphiphilic diblock copolymers exhibit a wide diversity of behavior upon poration, due to competitions between edge, surface and bending energies, while viscous dissipation mechanisms determine the time scales. The copolymers are essentially chemically identical, only varying in chain length (related to the membrane thickness d). For small d, we find large unstable pores and the resulting membrane fragments reassemble into vesicles within minutes. For large d, however, submicron pores form and are extremely long-lived. The results show that pore behavior depends strongly on d, suggesting that the relevant energies depend on d and pore size r in a more complexmanner than what is generally assumed. Further control over these systems would make them useful for numerous applications.Publication Adhesion of Polymer Vesicles(2005-07-06) Lin, John J.; Bates, Frank S.; Hammer, Daniel A; Silas, James A.The adhesion and bending modulus of polybutadiene-poly(ethylene oxide) block copolymer vesicles made from a bidisperse mixture of polymers is measured using micropipette aspiration. The adhesion energy between biotinylated vesicles and avidin beads is modeled by incorporating the extension of the adhesive ligands above the surface brush of the vesicle according to the blob model of bidisperse polymer mixtures of Komura and Safran assuming the polymer brush at the surface of the vesicle is compact. The same model accurately reproduces the scaling of the bending modulus with polymer composition.Publication The Shear Threshold Effect for Particle Adhesion to Bioreactive Surfaces: Influence of Receptor and Ligand Site Density(2003-03-22) Bhatia, Sujata K.; Hammer, Daniel ASelectins are cell adhesion molecules that mediate capture and rolling adhesion of white blood cells to vascular walls, an essential component of the inflammatory response. Adhesion through L-selectin requires a hydrodynamic shear stress above a threshold level, a phenomenon known as the shear threshold effect. We have reported that the shear threshold effect can he re-created in cell-free systems, in which microspheres coated with the carbohydrate ligand sialyl Lewis x (sLex) are perfused over L-selectin-coated surfaces. This paper extends the use of the cell-free system to determine the concurrent influence of receptor and ligand site density on the shear threshold effect. We find that the shear threshold effect diminishes with increasing levels of either L-selectin or sLex. At reduced site densities of either L-selectin or sLex, the shear threshold effect is present, with maximal rolling observed at a shear stress of 1.2 dynes/cm2. At higher site densities of L-selectin and sLex, the shear threshold effect disappears. These results suggest that the shear threshold relies on the formation of low numbers of receptor-ligand bonds.Publication Interplay between Rolling and Firm Adhesion Elucidated with a Cell-Free System Engineered with Two Distinct Receptor-Ligand Pairs(2003-10-01) Eniola, A. Omolola; Willcox, P. Jeanene; Hammer, Daniel AThe firm arrest of leukocytes to the endothelium during inflammation is known to be mediated by endothelial intercellular adhesion molecules (ICAMs) binding to activated integrins displayed on leukocyte surface. Selectin-ligand interactions, which mediate rolling, are believed to be important for facilitating firm adhesion, either by activating integrins or by facilitating the transition to firm adhesion by making it easier for integrins to bind. Although leukocytes employ two distinct adhesion molecules that mediate different states of adhesion, the fundamental biophysical mechanisms by which two pairs of adhesion molecules facilitate cell adhesion is not well understood. In this work, we attempt to understand the interaction between two molecular systems using a cell-free system in which polystyrene microspheres functionalized with the selectin ligand, sialyl LewisX (sLeX), and an antibody against ICAM-1, aICAM-1, are perfused over P-selectin/ICAM-1 coated surfaces in a parallel plate flow chamber. Separately, sLeX/P-selectin interactions support rolling and aICAM-1/ICAM-1 interactions mediate firm adhesion. Our results show that sLeX/aICAM-1 microspheres will firmly adhere to P-selectin/ICAM-1 coated surfaces, and that the extent of firm adhesion of microspheres is dependent on wall shear stress within the flow chamber, sLeX/aICAM-1 microsphere site density, and P-selectin/ICAM-1 surface density ratio. We show that P-selectin’s interaction with sLeX mechanistically facilitates firm adhesion mediated by antibody binding to ICAM-1: the extent of firm adhesion for the same concentration of aICAM-1/ICAM-1 interaction is greater when sLeX/P-selectin interactions are present. aICAM-1/ICAM-1 interactions also stabilize rolling by increasing pause times and decreasing average rolling velocities. Although aICAM-1 is a surrogate for β2-integrin, the kinetics of association between aICAM-1 and ICAM-1 is within a factor of 1.5 of activated integrin binding ICAM-1, suggesting the findings from this model system may be insightful to the mechanism of leukocyte firm adhesion. In particular, these experimental results show how two molecule systems can interact to produce an effect not achievable by either system alone, a fundamental mechanism that may pervade leukocyte adhesion biology.Publication I-Domain of Lymphocyte Function-Associated Antigen-1 Mediates Rolling of Polystyrene Particles on ICAM-1 under Flow(2005-11-01) Eniola, A. Omolala; Krasik, Ellen F; Smith, Lee A; Song, Gang; Hammer, Daniel AIn their active state, ß2-integrins, such as LFA-1, mediate the firm arrest of leukocytes by binding intercellular adhesion molecules (ICAMs) expressed on endothelium. Although the primary function of LFA-1 is assumed to be the ability to mediate firm adhesion, recent work has shown that LFA-1 can contribute to cell tethering and rolling under hydrodynamic flow, a role previously largely attributed to the selectins. The inserted (I) domain of LFA-1 has recently been crystallized in the wildtype (wt) and locked-open conformations and has been shown to, respectively, support rolling and firm adhesion under flow when expressed in αLß2 heterodimers or as isolated domains on cells. Here, we report results from cell-free adhesion assays where wt I-domain-coated polystyrene particles were allowed to interact with ICAM-1-coated surfaces in shear flow. We show that wt I-domain can independently mediate the capture of particles from flow and support their rolling on ICAM-1 surfaces in a manner similar to how carbohydrate-selectin interactions mediate rolling. Adhesion is specific and blocked by appropriate antibodies. We also show that the rolling velocity of I-domain-coated particles depends on the wall shear stress in flow chamber, I-domain site density on microsphere surfaces, and ICAM-1 site density on substrate surfaces. Furthermore, we show that rolling is less sensitive to wall shear stress and ICAM-1 substrate density at high density of I-domain on the microsphere surface. Computer simulations using adhesive dynamics can recreate bead rolling dynamics and show that the mechanochemical properties of ICAM-1-I-domain interactions are similar to those of carbohydrate-selectin interactions. Understanding the biophysics of adhesion mediated by the I-domain of LFA-1 can elucidate the complex roles this integrin plays in leukocyte adhesion in inflammation.Publication Differential Adhesion of Microspheres Mediated by DNA Hybridization I: Experiment(2006-03-13) Zhang, Ying; Graves, David J; Milam, Valeria T; Hammer, Daniel AWe have developed a novel method to study collective behavior of multiple hybridized DNA chains by measuring the adhesion of DNA-coated micron-scale beads under hydrodynamic flow. Beads coated with single-stranded DNA probes are linked to surfaces coated with single target strands through DNA hybridization, and hydrodynamic shear forces are used to discriminate between strongly and weakly bound beads. The adhesiveness of microspheres depends on the strength of interaction between DNA chains on the bead and substrate surfaces, which is a function of the degree of DNA chain overlap, the fidelity of the match between hybridizing pairs, and other factors that affect the hybridization energy, such as the salt concentration in the hybridization buffer. The force for bead detachment is linearly proportional to the degree of chain overlap. There is a detectable drop in adhesion strength when there is a single base mismatch in one of the hybridizing chains. The effect of single nucleotide mismatch was tested with two different strand chemistries, with mutations placed at several different locations. All mutations were detectable, but there was no comprehensive rule relating the drop in adhesive strength to the location of the defect. Since adhesiveness can be coupled to the strength of overlap, the method holds promise to be a novel methodology for oligonucleotide detection.Publication The Effect of Cellular Receptor Diffusion on Receptor-Mediated Viral Binding Using Brownian Adhesive Dynamics (BRAD) Simulations(2005-03-01) English, Thomas J.; Hammer, Daniel ABrownian adhesive dynamics (BRAD) is a new method for simulating the attachment of viruses to cell surfaces. In BRAD, the motion of the virus is subject to stochastic bond formation and breakage, and thermal motion owing to collisions from the solvent. In the model, the virus is approximated as a rigid sphere and the cell surface is approximated as a rigid plane coated with receptors. In this article, we extend BRAD to allow for the mobility of receptors in the plane of the membrane, both before and after they are ligated by viral attachment proteins. Allowing the proteins to move within the membrane produced several differences in behavior from when the receptors are immobilized. First, the mean steady-state bond number is unaffected by changes in cellular receptor density because proteins are now free to diffuse into the contact area, and the extent of binding is dictated by the availability of viral attachment proteins. Second, the time required to reach steady-state binding increases as both the cellular receptor number decreases and the receptor mobility decreases. This is because receptor diffusion is a slower process than the binding kinetics of the proteins. Decreasing the rate of protein binding was found to decrease the fraction of viruses bound to steady state, but not the extent of binding for those viruses that were bound. Increasing the binding rate increased the fraction of viruses bound, until no further viruses could bind. Alterations in receptor binding kinetics had no discernable effect on the mean steady-state bond number between virus and cell, because interactions were of sufficiently high affinity that all available receptor-viral attachment proteins were destined to bind at steady state.Publication Multiparticle Adhesive Dynamics. Interactions between Stably Rolling Cells(2001-08-01) King, Michael R; Hammer, Daniel AA novel numerical simulation of adhesive particles (cells) reversibly interacting with an adhesive surface under flow is presented. Particle–particle and particle–wall hydrodynamic interactions in low Reynolds number Couette flow are calculated using a boundary element method that solves an integral representation of the Stokes equation. Molecular bonds between surfaces are modeled as linear springs and stochastically formed and broken according to postulated descriptions of force-dependent kinetics. The resulting simulation, Multiparticle Adhesive Dynamics, is applied to the problem of selectin-mediated rolling of hard spheres coated with leukocyte adhesion molecules (cell-free system). Simulation results are compared to flow chamber experiments performed with carbohydrate-coated spherical beads rolling on P-selectin. Good agreement is found between theory and experiment, with the main observation being a decrease in rolling velocity with increasing concentration of rolling cells or increasing proximity between rolling cells. Pause times are found to increase and deviation motion is found to decrease as pairs of rolling cells become closer together or align with the flow.