James L. Cornette

Computational determination of side chain specificity for pockets in class I MHC molecules

We show that a rapidly executable computational procedure provides the basis for a predictive understanding of antigenic peptide side chain specificity, for binding to class I major histocompatibility complex (MHC) molecules. The procedure consists of a combined search to identify the joint conformations of peptide side chains and side chains comprising the MHC pocket, followed by conformational selection, using a target function, based on solvation energies and modified electrostatic energies. The method was applied to the B pocket region of five MHC molecules, which were chosen to encompass the full range of specificities displayed by anchors at peptide position 2. These were a medium hydrophobic residue (Leu or Met) for HLA-A*0201, a basic residue (Arg or Lys) for HLA-B*2705; a small hydrophobic residue (Val) for HLA-A*6801, an acidic residue (Glu) for HLA-B*4001 and a bulky residue (Tyr) for H-2K(d). The observed anchors are correctly predicted in each case. The agreement for HLA-B40 and H-2K(d) is especially promising, since their structures have not yet been determined experimentally. Because the experimental determination of motifs by elution is difficult and these calculations take only hours on a high speed workstation, the results open the possibility of routine determination of motifs computationally.

Gauss-Vaníček and Fourier Transform Spectral Analyses of Marine Diversity

This article shows that Gauss-Vanick (GV) analysis of this diversity data detrended with a cubic also strongly signals a 62-million-year periodicity. Furthermore, it was found that neither GV analysis nor Fourier transform analysis of the nondetrended data leads to any statistically significant periodicity. The results show that the two techniques are equivalent.

Subpopulations of Equine Infectious Anemia Virus Rev Coexist In Vivo and Differ in Phenotype

ABSTRACT Lentiviruses exist in vivo as a population of related, nonidentical genotypes, commonly referred to as quasispecies. The quasispecies structure is characteristic of complex adaptive systems and contributes to the high rate of evolution in lentiviruses that confounds efforts to develop effective vaccines and antiviral therapies. Here, we describe analyses of genetic data from longitudinal studies of genetic variation in a lentivirus regulatory protein, Rev, over the course of disease in ponies experimentally infected with equine infectious anemia virus. As observed with other lentivirus data, the Rev variants exhibited a quasispecies character. Phylogenetic and partition analyses suggested that the Rev quasispecies comprised two distinct subpopulations that coexisted during infection. One subpopulation appeared to accumulate changes in a linear, time-dependent manner, while the other evolved radially from a common variant. Over time, the two subpopulations cycled in predominance coincident with changes in the disease state, suggesting that the two groups differed in selective advantage. Transient expression assays indicated the two populations differed significantly in Rev nuclear export activity. Chimeric proviral clones containing Rev genotypes representative of each population differed in rate and overall level of virus replication in vitro. The coexistence of genetically distinct viral subpopulations that differ in phenotype provides great adaptability to environmental changes within the infected host. A quasispecies model with multiple subpopulations may provide additional insight into the nature of lentivirus reservoirs and the evolution of antigenic and drug-resistant variants.

PAQ: Partition Analysis of Quasispecies

MOTIVATION The complexities of genetic data may not be accurately described by any single analytical tool. Phylogenetic analysis is often used to study the genetic relationship among different sequences. Evolutionary models and assumptions are invoked to reconstruct trees that describe the phylogenetic relationship among sequences. Genetic databases are rapidly accumulating large amounts of sequences. Newly acquired sequences, which have not yet been characterized, may require preliminary genetic exploration in order to build models describing the evolutionary relationship among sequences. There are clustering techniques that rely less on models of evolution, and thus may provide nice exploratory tools for identifying genetic similarities. Some of the more commonly used clustering methods perform better when data can be grouped into mutually exclusive groups. Genetic data from viral quasispecies, which consist of closely related variants that differ by small changes, however, may best be partitioned by overlapping groups. RESULTS We have developed an intuitive exploratory program, Partition Analysis of Quasispecies (PAQ), which utilizes a non-hierarchical technique to partition sequences that are genetically similar. PAQ was used to analyze a data set of human immunodeficiency virus type 1 (HIV-1) envelope sequences isolated from different regions of the brain and another data set consisting of the equine infectious anemia virus (EIAV) regulatory gene rev. Analysis of the HIV-1 data set by PAQ was consistent with phylogenetic analysis of the same data, and the EIAV rev variants were partitioned into two overlapping groups. PAQ provides an additional tool which can be used to glean information from genetic data and can be used in conjunction with other tools to study genetic similarities and genetic evolution of viral quasispecies.

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.

Triacylglycerol assembly from binary mixtures of fatty acids byApiotrichum curvatum

To observe how the stereospecific distribution of acyl groups in triglycerides is affected by the composition of fatty acids available for esterification, the oleaginous yeastApiotrichum curvatum was grown on various binary mixture of palmitic, stearic, oleic and linoleic acids as carbon sources, and the yeast triglycerides were analyzed. When oleic acid-linoleic acid mixtures in various ratios were used as substrates, the yeast grew well, and the composition of the intracellular triglycerides reflected the substrate composition, but more linoleate than oleate was deposited in the triglycerides. Oleate was favored over linoleate at thesn-2 position of the glycerol. With substrates containing palmitic and stearic acids, the yeast accumulated less oil, and incorporation of stearic acid into the triglycerides also was very limited. When mixtures of palmitic acid-oleic acid and palmitic acid-linoleic acid were used as substrates, the yeast triglyceride composition did not reflect that of the substrate, and the accumulation in the yeast of the unsaturated acid in the substrate was favored. Possibly, the yeast had more limited access to solid than to liquid substrates. For oleic acid-linoleic acid substrates, when the percentages of oleate and linoleate at the three glycerol positions were plottedvs. the percentage of these acyl groups in the total triglyceride, apparent linear relations were observed for most of the range, and the sums of the intercepts and slopes of the three lines for each acyl group were 0 and 3, respectively. Two mathematical models of triglyceride assembly are proposed, both of which fit the experimental data. One model assumes that for a certain proportion of the glycerol molecules, the acyl composition of the threesn positions is rigidly controlled independently of the substrate concentration. The other assumes that the various acyl groups are distributed on the threesn positions of glycerol with different affinities.

Identification of T-cell epitopes and use in construction of synthetic vaccines.

The T cell is central to the immune system response to foreign antigens, and understanding the mechanism of T cell response to antigen is crucial for vaccine development. Short subpeptides of foreign antigen can prime the T cells to respond to the whole antigen, in some cases as well as or better than immunization with the whole antigen itself. Antigenic sites located first in the murine model are also antigenic in the human, suggesting that the structural features of antigenic sites are species-independent. The amphipathic helix hypothesis has proven useful in developing an algorithm that has successfully located immunodominant sites in important proteins, thus reducing substantially the experimental time and effort required to locate those sites. Other algorithms have also been used successfully, but in all cases there are proven T-cell sites not accounted for by the algorithm. A data base showing T-cell response to collections of peptides uniformly distributed along protein antigens would be very useful in subsequent efforts to characterize the physical and chemical properties of T-cell antigenic sites.

Some basic elements of continuous selection models

Abstract We present a general framework for the discussion of continuous population genetic models of monoecious diploid populations that incorporate one or more of age structure, mortality selection, mating structure, and fertility of matings. Within this framework, we then develop the specific models recently presented by Charlesworth (1970 , Models 1 and 2) and Nagylaki and Crow (1974) and establish conditions under which the Malthusian parameters of these papers are equivalent.

Deterministic Genetic Models in Varying Environments

SummaryJ. B. S. Haldane and S. D. Jayakar [J. Genet. 58, 237–242 (1963)] argue that, when genotype fitnesses fluctuate from generation to generation, if the geometric and arithmetic means of the fitnesses satisfy certain inequalities, there will be a protected polymorphism. Their assertions are biologically interesting, but their mathematical analysis is not sufficient to support their conclusions. We present a firm mathematical analysis and several examples that demonstrate the need for stronger hypotheses and, in some cases, weaker conclusions.

Characterization of a helper T cell epitope recognized by mice of a low responder major histocompatibility type

Most known helper T cell (Th) epitopes studied have naturally been immunodominant epitopes recognized by T cells from animals of high responder major histocompatibility complex (MHC) haplotype. We have previously found that most such immunodominant Th epitopes tend to be amphipathic alpha helices, that is, helices with hydrophobic residues on one side and hydrophilic residues on the other, and the corresponding peptide can usually elicit a response to the native protein. However, very few epitopes seen by MHC low responder T cells have been identified. Within the CNBr fragment of residues 1-55 of sperm whale myoglobin (SwMb), a Th epitope is known to exist that stimulates T cells from low responder H-2k mice, but it has not yet been localized to a length of 8-12 residues, the usual length of a Th epitope. To determine whether this low responder epitope would have similar properties, we located it using 10 evenly overlapping 15-residue peptides that span the region. Analysis of this region by the computer program predicted the site covered by two peptides (residues 26-40 and 31-45 which overlap by 10 residues) to be the most likely site for a Th epitope. Of the 10 peptides tested experimentally, only one peptide (residues 26-40) was able to stimulate two low responder Th clones that are specific for the 1-55 region. The peptide was able to prime T cells of low responder B10.BR mice in vivo for in vitro response to the native SwMb as well as to the peptide fragment of residues 1-55. Immunization of low responder mice with SwMb showed that, of the 10 overlapping peptides, the major site of response within the 1-55 region is to the identified peptide. Finally, an extended peptide of residues 24-42 was made to increase the amphipathic score. This extended peptide induced greater proliferation of the clones. Thus, this low responder epitope has properties similar to those of immunodominant epitopes recognized by high responders.