Biomedical subjects

C DeLisi

Publications and source records attributed to C DeLisi.

At least 37 records · Page 2Linked to original sources

PubMed1996

HLA allele selection for designing peptide vaccines.

A central problem in developing vaccines against rapidly evolving viruses such as HIV and Influenza is the mutability of their antigens. In principle, the problem can be mitigated by using peptides from conserved portions of viral proteins. However, because cytotoxic T lymphocytes (CTLs), which such vaccines would stimulate, recognize pathogenic peptides only in association with class I products of the Major Histocompatibility Complex (MHC), and because human leukocyte antigen genes (HLA; the human MHC) are highly polymorphic, a peptide vaccine would have to bind a number of different HLA products. A natural question then, which is pertinent to the safety of the vaccine is, which HLA molecules should be targeted to achieve a prespecified coverage (say 90%) of a population. Taking account of disequilibrium between linked HLA loci, we identify 3-6 class I HLA alleles, depending on ethnic group, which cover about 90% of the population. While this leaves large numbers of individuals uncovered, a high level of herd immunity, and hence eradication of the virus, can be achieved through such a vaccine.

Alleles↗

PubMed1996

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.

Amino Acid Sequence↗

PubMed1995

Periodic variation in side-chain polarities of T-cell antigenic peptides correlates with their structure and activity.

We present an analysis that synthesizes information on the sequence, structure, and motifs of antigenic peptides, which previously appeared to be in conflict. Fourier analysis of T-cell antigenic peptides indicates a periodic variation in amino acid polarities of 3-3.6 residues per period, suggesting an amphipathic alpha-helical structure. However, the diffraction patterns of major histocompatibility complex (MHC) molecules indicate that their ligands are in an extended non-alpha-helical conformation. We present two mutually consistent structural explanations for the source of the alpha-helical periodicity, based on an observation that the side chains of MHC-bound peptides generally partition with hydrophobic (hydrophilic) side chains pointing into (out of) the cleft. First, an analysis of haplotype-dependent peptide motifs indicates that the locations of their defining residues tend to force a period 3-4 variation in hydrophobicity along the peptide sequence, in a manner consistent with the spacing of pockets in the MHC. Second, recent crystallographic determination of the structure of a peptide bound to a class II MHC molecule reveals an extended but regularly twisted peptide with a rotation angle of about 130 degrees. We show that similar structures with rotation angles of 100-130 degrees are energetically acceptable and also span the length of the MHC cleft. These results provide a sound physical chemical and structural basis for the existence of a haplotype-independent antigenic motif which can be particularly important in limiting the search time for antigenic peptides.

Antigens↗

PubMed1995

Flexible docking of peptides to class I major-histocompatibility-complex receptors.

We present a new method for docking flexible peptides to class I Major-Histocompatibility-Complex (MHC) receptors. Docking is performed in two steps: (a) The charged terminal peptide residues are located by randomly distributing multiple copies of each in volumes of approximately 150 A at either end of the binding groove, and then minimizing the system energy using a modified multiple-copy search algorithm. This is followed by (b) construction of the intervening chain using the multiple-copy bond-scaling-relaxation loop closure algorithm. In both steps, the copies tend to cluster and the size of the resulting clusters is proportional to the basin of attraction of the corresponding energy well. We show that native MHC-bound peptides have broad minima and, consequently, that misfolded, low-energy peptide conformations can be eliminated by restricting consideration to groups of peptides which cluster into broad minima. The accuracy of the method is assessed by comparing the predictions with crystallographic data for three different MHC peptide systems, at various degrees of stringency: (a) the extent to which we can determine side chain function (anchor vs. T-cell epitopes); (b) the extent to which we can determine the peptide-receptor orientation; and (c) the accuracy with which we can predict atomic coordinates. We find the method correct on (a) for 19 of the 22 non-Gly positions; the failures appearing to be a consequence of omitting solvation. Predictions related to (b) are also very encouraging, with the overall orientation of the predicted peptides being very similar to the crystal conformation, when measured by the hydrogen bonding pattern between the two. The degree of success in predicting atomic coordinates varied considerably, however, from 1.4 A for the HLA-A2 peptide to 2.7 A for the Kb peptide. The inaccuracy of the latter appears to reflect an incomplete target function, most likely the ommission of solvation. The calculations thus define the current limits of accuracy in docking flexible peptides to Class I receptors and identify the methodological improvements that must be made for the next advance in accuracy.

Algorithms↗

PubMed1995

Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments.

Hydrophobicity values for amino acids obtained from protein unfolding experiments are about twice as large as those obtained from data on the partitioning of amino acids between water and octanol. Quantitative analyses of several data sets, presented here, indicate that the difference is best explained by the most direct hypothesis, i.e. that the environment of hydrophobic groups in the interior of a protein is poorly modeled by octanol. Instead, we propose--and provide supporting evidence--that hydrocarbons are a more suitable model. First, we reanalyze data from both solute partitioning and protein unfolding experiments, taking account of the effects that were omitted previously, by introducing a volume dependence in the former and a full free energy analysis in the latter. Both changes in evaluation methodology decrease the discrepancy, but the differences remain substantial. The hydrophobicity parameter obtained from side-chain transfers between octanol and water increases from 16.7 to 22 cal/mol/Angstrom2, while that obtained from protein unfolding decreases from 34.9 to 31.2 cal/mol/Angstrom2. On the other hand, our analysis of the solubilities of pure hydrocarbons in water provides a hydrophobicity parameter of 30.8 cal/mol/Angstrom2. This apparent hydrocarbon-like environment of a protein's interior is also suggested more directly by an analysis of the contact environment of hydrophobic side chains in mutation/unfolding experiments, which have polar contact areas that are <2% of the total.

Amino Acids↗

PubMed1995

Flexible docking and design.

Docking and design are the major computational steps toward understanding and affecting receptor-ligand interactions. The flexibility of many ligands makes these calculations difficult and requires the development and use of special methods. The need for such tools is illustrated by two examples: the design of protease inhibitors and the analysis and design of peptide antigens binding to specific MHC receptors. We review the computational concepts that have been extended from rigid-body to flexible docking, as well as the following important strategies for flexible docking and design: (a) Monte Carlo/molecular dynamics docking, (b) in-site combinatorial search, (c) ligand build-up, and (d) site mapping and fragment assembly. The use of empirical free energy as a target function is discussed. Due to the rapid development of the methodology, most new methods have been tested on only a limited number of applications and are likely to improve results obtained by more traditional computational or graphic tools.

Algorithms↗

PubMed1994

Effect of conformational flexibility and solvation on receptor-ligand binding free energies.

A coherent framework is presented for determining the free energy change accompanying ligand binding to protein receptors. The most important new feature of the method is the contribution of the flexibility of the free ligand, and hence its conformational change on binding, to the free energy. Flexibility introduces two additional terms in the free energy difference: the internal energy difference between the ligand in the bound and free states and the backbone entropy loss. The former requires taking explicit account of the difference in solvation of the various forms of the free ligand. The solvation free energy change is estimated using an atomic solvation parameter model [Eisenberg & Mclachlan (1986) Nature 319, 199-203], with an improved parameter set. In order to evaluate the method, we applied it to three data sets for which increasingly general methods are required. The set to which the most restrictive theory can be applied consists of eight crystallized endopeptidase--protein inhibitor complexes which do not change conformation on binding and for which the major contribution to the solvation free energy is entropic. The results are in good agreement with the measured values and somewhat better than those previously reported in the literature. The second data set compares the relative binding free energies of biotin and its analogs for streptavidin. In this case the structures are also rigid, but solvation free energy must include both enthalpic and entropic components. We find that differential free energy predictions are approximately the same as those obtained by free energy perturbation techniques. The final application is an analysis of the measured stabilities of 13 different MHC receptor-peptide complexes. In this case we show that flexibility contributes 30-50% of the free energy change and find a correlation of 0.88 between our predicted free energies and peptide dissociation times.

Antigens, Viral↗

PubMed1994

Multiple copy sampling in protein loop modeling: computational efficiency and sensitivity to dihedral angle perturbations.

Multiple copy sampling and the bond scaling-relaxation technique are combined to generate 3-dimensional conformations of protein loop segments. The computational efficiency and sensitivity to initial loop copy dispersion are analyzed. The multicopy loop modeling method requires approximately 20-50% of the computational time required by the single-copy method for the various protein segments tested. An analytical formula is proposed to estimate the computational gain prior to carrying out a multicopy simulation. When 7-residue loops within flexible proteins are modeled, each multicopy simulation can sample a set of loop conformations with initial dispersions up to +/- 15 degrees for backbone and +/- 30 degrees for side-chain rotatable dihedral angles. The dispersions are larger for shorter and smaller for longer and/or surface loops. The degree of convergence of loop copies during a simulation can be used to complement commonly used target functions (such as potential energy) for distinguishing between native and misfolded conformations. Furthermore, this convergence also reflects the conformational flexibility of the modeled protein segment. Application to simultaneously building all 6 hypervariable loops of an antibody is discussed.

Animals↗

PubMed1994

Monte Carlo study of the effect of beta 2-microglobulin on the binding cleft of the HLA-A2 complex.

Peptide recognition by class I products of the major histocompatibility complex requires association of the class I heavy chain with beta 2-microglobulin. We present results of Monte Carlo simulations of the beta-pleated sheet floor of the human class I MHC molecule, HLA-A2, with and without beta 2-microglobulin. We find a significant effect of beta 2-microglobulin on the side chains of residues near a region that would accommodate the C-terminus of a bound peptide. By modeling simultaneously each loop and its neighboring strand at either end of the class I cleft, we find that beta 2-microglobulin restricts the conformational space of residues that are central to binding peptides. The effect is most pronounced for R97 and H114 and somewhat less important for Y99 and Y116, the latter forming strong hydrogen bonds with neighboring residues in the heavy chain itself.

Amino Acid Sequence↗

PubMed1993

Computing the structure of bound peptides. Application to antigen recognition by class I major histocompatibility complex receptors.

The ability to accurately compute the atomic positions of substrate-bound ligands is central to understanding biological recognition. Although substantial progress has been made in docking small, relatively rigid ligands, the problem of docking flexible peptides remains open. In this communication we present a new method that allows configurational flexibility of peptides, and apply it to predict the conformation of peptides bound to two class-I major histocompatibility complex receptors: human HLA-A2, and murine H-2Kb. Using only the approximate locations of the amino and carboxyl-terminal residues of the bound peptide, our calculations yield structures with backbone conformations that are similar to structures reported crystallographically.

Amino Acid Sequence↗

PubMed1993

Necessary conditions for avoiding incorrect polypeptide folds in conformational search by energy minimization.

Low energy conformations have been generated for melittin, pancreatic polypeptide, and ribonuclease S-peptide, both in the vicinity of x-ray structures by energy refinement and by an unconstrained search over the entire conformational space. Since the structural polymorphism of these medium-sized peptides in crystal and solution is moderate, comparing the calculated conformation to x-ray and nmr data provides information on local and global behavior of potential functions. Local analysis includes standardization calculations, which show that models with standard geometry can approximate good resolution x-ray data with less than 0.5 A rms deviation (RMSD). However, the atomic coordinates are shifted up to 2 A RMSD by local energy minimization, and thus 2 A is generally the smallest RMSD value one can target in a conformational search using the same energy evaluation models. The unconstrained search was performed by a buildup-type method based on dynamic programming. To accelerate the generation of structures in the conformational search, we used the ECEPP potential, defined in terms of standard polypeptide geometry. A number of low energy conformations were further refined by relaxing the assumption of standard bond lengths and bond angles through the use of the CHARMM potential, and the hydrophobic folding energies of Eisenberg and McLachlan were calculated. Each conformation is described in terms of the RMSD from the native, hydrogen-bonding structure, solvent-accessible surface area, and the ratio of surfaces corresponding to nonpolar and polar residues. The unconstrained search finds conformations that are different from the native, sometimes substantially, and in addition, have lower conformational energies than the native. The origin of deviations is different for each of the three peptides, but in all examples the refined x-ray structures have lower energies than the calculated incorrect folds when (1) the assumption of standard bond lengths and bond angles is relaxed; (2) a small and constant effective dielectric permittivity (epsilon < 10) is used; and (3) the hydrophobic folding energy is incorporated into the potential.

Amino Acid Sequence↗

PubMed1993

Determining protein loop conformation using scaling-relaxation techniques.

We recently developed a rapid loop closure algorithm in which bond lengths are scaled to constrain the ends of a segment to match a known distance and then gradually relaxed to their standard values, with boundary constraints maintained. Although the algorithm predicted the Zif286 zinc-finger loop to within approximately 2 A, it had a serious limitation that made its more general use tentative: it omitted the atomic environment of the loop. Here we report an extension of the algorithm to take into account the protein environment surrounding a given loop from the outset of the conformational search and show that it predicts structure with an efficiency and accuracy that could not be achieved without continuous environmental inclusion. The algorithm should be widely applicable to structure determination when complete experimental information is unavailable.

Algorithms↗

PubMed1993

Toward computational determination of peptide-receptor structure.

We introduce a method for docking small flexible ligands of the size of dipeptides and phosphocholine and test it against crystallographic complexes. We then show how the method can be used as the basis for a strategy for solving the much more difficult problem of docking fully flexible peptides in the 8-10-residue size range. After developing the method we apply it to peptide-MHC class I systems and find that the predictions are in accord with biological and crystallographic data.

Algorithms↗

PubMed1993

Graphical representations of the class I MHC cleft.

We describe computer graphics and computer aided manufacture of three-dimensional models designed specifically to elucidate the cleft in the class I human leukocyte antigen. The models evolve from computer graphical representations and provide a geometrically and chemically concise and detailed view of the antigen binding site. The techniques provide a new approach to representations of binding sites. The model provides sufficient detail to support binding specificities analysis of active sites involved in protein and DNA binding.

Binding Sites↗

PubMed1993

Role of conserved regions of class I MHC molecules in the activation of CD8+ cytotoxic T lymphocytes by peptide and purified cell-free class I molecules.

To analyze the molecular interactions involved in CD8+ cytotoxic T lymphocyte (CTL) recognition quantitatively, we developed a cell-free antigen presenting system. Genetically engineered soluble H-2Dd molecules coated on plastic microtiter plates could present HIV envelope peptide to an antigen-specific CTL clone, inducing it to produce IFN-gamma in the absence of accessory cells and their accessory or co-stimulatory molecules. The peptide-MHC complexes were functionally stable for over 24 h. The magnitude of T cell activation was dependent on the concentrations of both class I MHC molecule and the peptide, but was more sensitive to the concentration of the MHC molecule than to that of peptide. This result suggests that one MHC molecule can play more than one role in activating the CTL. One such role is the interaction between CD8 and a conserved region of class I MHC, as suggested by the finding that holding the total MHC concentration constant with an irrelevant class I MHC molecule (H-2Kb engineered to have the same alpha 3 domain as H-2Dd) made the T cell response less sensitive to the change in concentration of the relevant MHC molecule (H-2Dd). The irrelevant class I MHC molecule (H-2Kb), unable to present this peptide by itself, augmented the T cell response at lower concentrations of peptide. These results suggest that the conserved alpha 3 domain of the class I MHC heavy chain as well as polymorphic regions play an important role in T cell activation and that T cell interaction with MHC molecules not presenting peptide can still augment the response.

Amino Acid Sequence↗

PubMed1992

Impact of massively parallel computation on protein structure determination.

For the past two decades, an important paradigm in protein chemistry has been the assertion that a biologically active protein is at thermodynamic equilibrium and therefore adopts its minimum free energy structure. Although some evidence now suggests that not all proteins conform to this notion, it is true often enough to remain an important guiding principle in structure determination, whether by direct computation or by the computationally assisted approaches of diffraction and resonance. Among the difficulties in predicting structure from sequence are the lack of a useful potential function incorporating the influence of solvent and the inability to sample the phase space efficiently or even to determine whether a free energy minimum is, in fact, the global minimum. These problems are general. Although they are greatly mitigated by experimental information, they become increasingly severe as empirical constraints are reduced. We review the difficulties involved in the general problem of protein structure prediction and discuss the impact of increased computer power in the context of new approaches to solvation and parallel algorithm design. A general focus of our discussion is the need to understand the theoretical basis for effective theories and to accommodate in numerical methods the interplay of different temporal and spatial scales.

Algorithms↗

PubMed1991

Constrained optimization and protein structure determination.

Energy minimization is one of the main approaches to the computational determination of macromolecular structure. Due to the approximations in the empirical free-energy functions and due to the computational difficulties in locating their global minima, the problem is at present intractable when the only information available is the sequence of subunits forming the molecule. A less-demanding problem in terms of both physics and mathematics is constrained optimization, which uses additional but incomplete experimental information such as distances between certain atoms. This paper reviews methods for generating molecular structure using bond lengths and angles as variables and shows how the structure can be fully specified in terms of local geometry. The analysis permits precise statements to be made about the minimum set of distances that specify a unique structure without recourse to energy minimization. We then discuss the complementary situation, i.e., structure prediction with energy minimization based only on sequence information. Finally, we show how distance constraints can be incorporated into energy minimization methods.

Algorithms↗

PubMed1990

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.

Algorithms↗