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K Gulukota

Publications and source records attributed to K Gulukota.

5 recordsLinked to original sources
PubMed1998

Computational determination of the structure of rat Fc bound to the neonatal Fc receptor.

The available crystal structure for the complex between the Fc fragment of immunoglobulin G (IgG) and the neonatal Fc receptor (FcRn) was determined at low resolution and has no electron density for a large portion of the CH2 domain of the Fc. Here, we use a well validated computational docking algorithm in conjunction with known crystallographic data to predict the orientation of CH2 when bound to FcRn, and validate the predicted structure with data from site-specific mutagenesis experiments. The predicted Fc structure indicates that the CH2 domain moves upon binding FcRn , such that the end-to-end distance of the bound Fc fragment is greater than it is in the crystal structure of isolated Fc. The calculated orientation of the bound CH2 domain is displaced by an average of 6 A from the CH2 orientation in the structure of Fc alone, and shows improved charge complementarity with FcRn. The predicted effects of 11 specific mutations in Fc and FcRn are calculated and the results are compared with experimental measurements. The predicted structure is consistent with all reported mutagenesis data, some of which are explicable only on the basis of our model. The current study predicts that FcRn-bound Fc is asymmetric due to reorientation of the CH2 domain upon FcRn binding, a rearrangement that would be likely to interfere with optimal binding of FcRn at the second binding site of the Fc homodimer.

Animals↗
PubMed1997

Two complementary methods for predicting peptides binding major histocompatibility complex molecules.

Peptides that bind to major histocompatibility complex products (MHC) are known to exhibit certain sequence motifs which, though common, are neither necessary nor sufficient for binding: MHCs bind certain peptides that do not have the characteristic motifs and only about 30% of the peptides having the required motif, bind. In order to develop and test more accurate methods we measured the binding affinity of 463 nonamer peptides to HLA-A2.1. We describe two methods for predicting whether a given peptide will bind to an MHC and apply them to these peptides. One method is based on simulating a neural network and another, called the polynomial method, is based on statistical parameter estimation assuming independent binding of the side-chains of residues. We compare these methods with each other and with standard motif-based methods. The two methods are complementary, and both are superior to sequence motifs. The neural net is superior to simple motif searches in eliminating false positives. Its behavior can be coarsely tuned to the strength of binding desired and it is extendable in a straightforward fashion to other alleles. The polynomial method, on the other hand, has high sensitivity and is a superior method for eliminating false negatives. We discuss the validity of the independent binding assumption in such predictions.

Artificial Intelligence↗
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↗
PubMed1994

Statistical mechanics of kinetic proofreading in protein folding in vivo.

The statistical energy landscape picture of protein folding has led to the understanding that the energy landscape must have guiding forces leading to a protein folding funnel in order to avoid the Levinthal paradox in vitro. Since folding in vivo often requires the action of chaperone molecules and ATP hydrolysis, we must ask whether folding in a system maintained away from equilibrium can avoid the Levinthal paradox in other ways. We describe a model of the action of chaperone molecules in protein folding in vivo on the basis of a repetitive cycle of binding and unbinding, allowing the possibility of kinetic proofreading. We also study models in which chaperone binding is locally biased, depending on the similarity of the conformation to the native one. We show that while kinetic proofreading can modestly facilitate folding, it is insufficient by itself to overcome the Levinthal paradox. On the other hand, such kinetic proofreading with biasing can provide the nonequilibrium analog of a folding funnel and greatly enhance folding yields and speed up folding.

Chaperonins↗