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C DeLisi

Publications and source records attributed to C DeLisi.

106 records · Page 6Linked to original sources
PubMed1976

Some physical chemical aspects of receptor-ligand interactions.

Quantitative evaluations of a variety of binding reactions of interest to immunologists have usually assumed that the reactants are homogenously dispersed in solution for purposes of calculation. In fact, many of these reactions involve cell-bound "receptors" which are present at exceedingly high local concentrations on discrete particles. We describe how such a distribution can influence the experimentally measured binding constants. We also briefly consider the additional complexities introduced when multipoint attachment between the ligand and cell-bound receptors is possible, and discuss the possible biological implications.

Binding Sites, Antibody↗
PubMed1976

Hemolytic plaque inhibition: the physical chemical limits on its use as an affinity assay.

An analysis of the fundamental physical chemical limits of hemolytic plaque inhibition as a method for obtaining thermodynamic and kinetic information is presented. It is shown that inhibition curve characteristics will be sensitive functions of reaction affinities only when the antibody inhibitor and antibody red blood cell reaction mechanisms are related in certain ways. It is further shown that conditions which are most sensititive to IgG affinity changes will generally not be the best for detecting changes in IgM affinity. The apparently conflicting reports on IgM maturation are completely explicable in terms of experimental requirements imposed by physical chemical characteristics of the reaction. Experiments in which maturation is observed are found to conform to the most sensitive conditions of the assay, whereas those in which it is not observed are found to conform to relatively insensitive conditions, and would therefore be capable of registering changes only when affinity shifts are large.

Binding Sites, Antibody↗
PubMedDate not supplied

A theory of measurement error and its implications for spatial and temporal gradient sensing during chemotaxis.

In order that cells respond to environmental cues, they must be able to measure ambient ligand concentration. Concentrations fluctuate, however, because of thermal noise, and one can readily show that estimates based on concentration values at a particular moment will be subject to substantial error. Cells are therefore expected to average their estimates over some limited time period. In this paper we assume that a cell uses fractional receptor occupancy as a measure of ambient ligand concentration and develop general expressions for the error a cell makes because the length of the averaging period is necessarily limited. Our analysis is general, relieving many of the assumptions underlying the seminal work of Berg and Purcell. The most important formal difference is our inclusion of occupancy-dependent dissociation--a phenomenon that has been well-documented for many systems. In addition, our formulation permits signal averaging to begin before chemical equilibrium has been established and it allows binding kinetics to be nonlinear (i.e., biomolecular rather than pseudo-first-order). The results are applied to spatial and temporal concentration gradients. In particular we estimate the minimum averaging times required for cells to detect such gradients under typical in vitro conditions. These estimates involve assigning numerical values to receptor ligand rate constants. If the rate constants are at their maximum possible values (limited only by center of mass diffusion), then either temporal or spatial gradients can be detected in minutes or less. If, however, as suggested by experiments, the rate constants are several orders of magnitude below their diffusion-limited values, then under typical constant gradient conditions the time required to detect a spatial gradient is prohibitively long, whereas temporal gradients can still be detected in reasonable lengths of time. This result was obtained for large cells such as lymphocytes, as well as for the smaller, bacterial cells. The ratio of averaging times for the two mechanisms--amounting to several orders of magnitude--is well beyond what could be reconciled by limitations of the calculation, and strongly suggests heavy reliance on temporal sensing mechanisms under typical in vitro conditions with constant spatial gradients.

Animals↗
PubMedDate not supplied

Some mathematical aspects of mapping DNA cosmids.

A number of experimental and mathematical problems must be solved before high resolution physical maps of mammalian chromosomes can be reliably determined. Such a map might consist of an ordered set of nonsequenced, overlapping DNA fragments 20,000-40,000 bases long, produced by digestion of a chromosome, using two restriction enzymes. Map construction requires assigning a signature to each fragment that differentiates it unambiguously from every other fragment, and then devising a computationally efficient algorithm that will provide a unique ordering of the fragments. In the first part of this paper we present a polynomial time algorithm that yields a unique map, and is largely independent of the method for assigning signatures. In the next section we analyze the distribution of lengths of restriction digest fragments and discuss the implications for the algorithm, including the expected number of map gaps. Finally, we discuss a specific method for assigning signatures proposed by Hans Lehrach, based on which of a panel of probes binds to a given fragment. In particular we examine the effects of fragment length heterogeneity on the theoretical optimum length and number of probes, and the extent to which false signatures might be obtained by nonspecific binding. We conclude that the Lehrach strategy is effective provided the number of probes is greater than or equal to 150, but that each fragment will need testing with at most 25 probes.

Algorithms↗
PubMedDate not supplied

The organization of human leucocyte antigen class I epitopes in HIV genome products: implications for HIV evolution and vaccine design.

Knowledge of human leucocyte antigen (HLA) peptide binding motifs permits rapid selection of candidate viral protein fragments for induction of T cell-mediated immunity. A search for HLA class I peptide binding motifs in structural proteins of human immunodeficiency virus (HIV) of different genetic lineages provides a map of the genetic organization of potential T cell antigenic sites, and at the same time identifies all motifs in highly conserved regions of HIV-1 env, gag and pol. The density of motifs is anomalous at both the high and low end of the spectrum: local organization is characterized by clustering in relatively short regions, while large scale organization is characterized by anomalously long runs between motifs. The former is expected simply due to the fact that motifs often have overlapping anchor residue sets. A detailed statistical analysis of the latter, however, shows that the length of the runs cannot be accounted for by chance alone. Although motif clusters show no preference to be in either conserved or variable regions, low motif density stretches occur preferentially in variable portions of the protein sequence, which suggests that the virus may be mutating to evade the cellular arm of the immune system.

AIDS Vaccines↗