Biomedical subjects

Daniel Coombs

Publications and source records attributed to Daniel Coombs.

10 recordsLinked to original sources

PubMed2006

A theoretical and experimental study of competition between solution and surface receptors for ligand in a Biacore flow cell.

Rate constants that characterize the kinetics of binding and dissociation between biomolecules carry fundamental information about the biological processes these molecules are involved in. An instrument that is widely used to determine these rate constants is the Biacore. In a Biacore experiment, one of the reactants, which we will call the receptor, is immobilized on a sensor chip. During the binding phase of the experiment the other reactant flows past the chip. After binding, buffer alone is introduced into the flow cell and dissociation is monitored. Often surface-based binding assays are influenced by the transport of the reactant in solution, complicating the determination of the chemical rate constants from the observed binding kinetics. We propose a new way to determine the dissociation rate constant by adding soluble receptor during dissociation. The method is tested first on simulated data and then on Biacore experiments where the lac repressor protein binds and dissociates from a stretch of double stranded DNA containing the lac repressor binding site. With this method we find a dissociation rate constant k(d)=0.075 +/- 0.005s(-1), a value that is faster than previously obtained from Biacore experiments. In developing our method to analyze these experiments we obtain an expression for the transport limited rate constant for a Biacore experiment when soluble receptor is present during dissociation.

Biosensing Techniques↗

PubMed2006

Analysis of peptide/MHC-induced TCR downregulation: deciphering the triggering kinetics.

The interaction of T-lymphocytes with antigen-presenting cells displaying a small number of specific peptide/major histocompatibility complexes results in the downregulation of a large number of T-cell receptors (TCR), suggesting serial TCR triggering. However, the details of TCR downregulation are controversial. In particular, the level of comodulation of nonengaged TCR reported by different authors ranges from essentially none to considerable levels. Here, we address this controversy using complementary experimental and mathematical techniques. We find that TCR downregulation is very rapid during the first 2-4 min after T-cell antigen-presenting cells contact formation. After this phase, TCR downregulation proceeds at a relatively slow rate. Statistical and computational analyses show that this pronounced change in downregulation kinetics is compatible with the notion of initial serial triggering of clustered TCR followed by serial triggering of individual TCR. We further propose a compatible mechanism for concurrent triggering of multiple TCR by a single peptide/major histocompatibility complex. We provide a unified picture of productive TCR engagement and downregulation in which TCR triggering characteristics evolve from an initial cooperative phase to a sustained phase of signal accumulation.

Antigen-Presenting Cells↗

PubMed2005

Evolution of virulence: interdependence, constraints, and selection using nested models.

Natural selection acts on virus populations at two distinct but interrelated levels: within individual hosts and between them. Studies of the evolution of virulence typically focus on selection acting at the epidemiological or between-host level and demonstrate the importance of trade-offs between disease transmission and virulence rates. Within-host studies reach similar conclusions regarding trade-offs between transmission and virulence at the level of individual cells. Studies which examine selection at both scales assume that between- and within-host selection are necessarily in conflict. We explicitly examine these ideas and assumptions using a model of within-host viral dynamics nested within a model of between-host disease dynamics. Our approach allows us to evaluate the direction of selection at the within- and between-host levels and identify situations leading to conflict and accord between the two levels of selection.

Host-Parasite Interactions↗

PubMed2005

T cell receptor binding kinetics required for T cell activation depend on the density of cognate ligand on the antigen-presenting cell.

CD8(+) T cells recognize peptides of eight to nine amino acid residues long in the context of MHC class I molecules on the surface of antigen-presenting cells (APCs). This recognition event is highly sensitive, as evidenced by the fact that T cells can be activated by cognate peptide/MHC complex (pMHC) at extremely low densities (1-50 molecules). High sensitivity is particularly valuable for detection of antigens at low density, such as those derived from tumor cells and intracellular pathogens, which can down-modulate cognate pMHCs from the surface of APCs to evade recognition by the adaptive immune system. T cell activation is only triggered in response to interactions between the T cell receptor (TCR) and the pMHC ligand that reach a specific half-life threshold. However, interactions with excessively long half-lives result in impaired T cell activation. Thus, efficient T cell activation by pMHC on the surface of APCs requires an optimal dwell time of TCR-pMHC interaction. Here, we show that, although this is a requirement at low cognate pMHC density on the APC surface, at high epitope density there is no impairment of T cell activation by extended TCR-pMHC dwell times. This observation was predicted by mathematical simulations for T cell activation by pMHC at different densities and supported by experiments performed on APCs selected for varied expression of cognate pMHC. According to these results, effective T cell activation depends on a complex interplay between inherent TCR-pMHC binding kinetics and the epitope density on the APC.

Antigen-Presenting Cells↗

PubMed2004

Optimizing within-host viral fitness: infected cell lifespan and virion production rate.

We explore how an infected cell's virion production rate can affect the relative fitness of a virus within a host. We perform an invasion analysis, based on an age-structured model of viral dynamics, to derive the within-host relative viral fitness. We find that for chronic infections, in the absence of trade-offs between viral life history stages, natural selection favors viral strains whose virion production rate maximizes viral burst size. We then show how various life history trade-offs such as that between virion production and immune system recognition and clearance of virally infected cells can lead to natural selection favoring production rates lower than the one that maximizes burst size. Our findings suggest that HIV replication rates should vary between cells with different life spans, as has been suggested by recent observation.

Cells↗

PubMed2004

Equilibrium thermodynamics of cell-cell adhesion mediated by multiple ligand-receptor pairs.

In many situations, cell-cell adhesion is mediated by multiple ligand-receptor pairs. For example, the interaction between T cells and antigen-presenting cells of the immune system is mediated not only by T cell receptors and their ligands (peptide-major histocompatibility complex) but also by binding of intracellular adhesion molecules. Interestingly, these binding pairs have different resting lengths. Fluorescent labeling reveals segregation of the longer adhesion molecules from the shorter T cell receptors in this case. Here, we explore the thermal equilibrium of a general cell-cell interaction mediated by two ligand-receptor pairs to examine competition between the elasticity of the cell wall, nonspecific intercellular repulsion, and bond formation, leading to segregation of bonds of different lengths at equilibrium. We make detailed predictions concerning the relationship between physical properties of the membrane and ligand-receptor pairs and equilibrium pattern formation, and suggest experiments to refine our understanding of the system. We demonstrate our model by application to the T cell/antigen-presenting-cell system and outline applications to natural killer cell adhesion.

Binding Sites↗

PubMed2004

Effects of the geometry of the immunological synapse on the delivery of effector molecules.

Recent experiments focusing on the function of the immunological synapse formed between a T cell and an antigen-presenting cell raise many questions about its purpose. We examine the proposal that the close apposition of the cell membranes in the central region of the synapse acts to focus T-cell secretions on the target cell, thus reducing the effect on nearby cells. We show that the efficiency of targeted T-cell responses to closely apposed cells is only weakly dependent on the distance between the cells. We also calculate effective (diffusion-limited) rates of binding and unbinding for molecules secreted within the synapse. We apply our model to the stimulation of B cells by secreted interleukin-4 (IL-4), and find that very few molecules of IL-4 need be released to essentially saturate the IL-4 receptors on the B-cell surface.

Animals↗

PubMed2003

Optimal viral production.

Viruses reproduce by multiplying within host cells. The reproductive fitness of a virus is proportional to the number of offspring it can produce during the lifetime of the cell it infects. If viral production rates are independent of cell death rate, then one expects natural selection will favor viruses that maximize their production rates. However, if increases in the viral production rate lead to an increase in the cell death rate, then the viral production rate that maximizes fitness may be less than the maximum. Here we pose the question of how fast should a virus replicate in order to maximize the number of progeny virions that it produces. We present a general mathematical framework for studying problems of this type, which may be adapted to many host-parasite systems, and use it to examine the optimal virus production scheduling problem from the perspective of the virus.

Evolution, Molecular↗

PubMed2002

Activated TCRs remain marked for internalization after dissociation from pMHC.

To assess the roles of serial engagement and kinetic proofreading in T cell receptor (TCR) internalization, we have developed a mathematical model of this process. Our determination of TCR down-regulation for an array of TCR mutants, interpreted in the context of the model, has provided new information about peptide-induced TCR internalization. The amount of TCR down-regulation increases to a maximum value and then declines as a function of the half-life of the bond between the TCR and peptide-major histocompatibility complex (pMHC). The model shows that this behavior, which reflects competition between serial engagement and kinetic proofreading, arises only if it is postulated that activated TCRs remain marked for internalization after dissociation from pMHC. The model also predicts that because of kinetic proofreading, the range of TCR-pMHC-binding half-lives required for T cell activation depends on the concentrations and localization of intracellular signaling molecules. We show here that kinetic proofreading provides an explanation for the different requirements for activation observed in naïve and memory T cells.

Animals↗

PubMed2002

Periodic chirality transformations propagating on bacterial flagella.

When a helical bacterial flagellum, clamped at one end, is placed in an external flow, it has been observed that regions of the flagellum transform to the opposite chirality, and travel as pulses down the length of the filament, the process repeating periodically [H. Hotani, J. Mol. Biol. 156, 791 (1982)]]. We propose a theory for this phenomenon based on a treatment of the flagellum as an elastic object with multiple stable configurations. The simplest possible implementation of the model accurately reproduces key features seen in experiment.

Bacterial Physiological Phenomena↗