Barry D Olafson

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Class I major histocompatibility complex (MHC) molecules bind peptides derived from degraded proteins for display to T cells of the immune system. Peptides bind to MHC proteins with varying affinities, depending upon their sequence and length. We demonstrate that the thermal stability of the MHC-peptide complex depends directly on peptide binding affinity.(More)
Several rather different models of the Fe-o2 bond in oxyhemoglobin have previously been proposed, none of which provide a satisfactory explanation of several properties. We propose a new model for the bonding of an O2 to the Fe of myoglobin and hemoglobin and report ab initio generalized valence bond and configuration interaction calculations on FeO2 that(More)
NMR graf utilizes molecular mechanics and molecular dynamics simulation techniques, in conjunction with NOE and J-coupling data from NMR experiments, to quickly derive and analyze candidate structures of macromolecules. Test cases produce results within the experimental error bars of structures derived using x-ray crystallography.
From ab initio quality calculations on model systems, we conclude that in unliganded Fe-porphyrin the FE lies in the plane for both the high-spin (q) and intermediate-spin (t) states. Thus, the high-spin d6 Fe is not too big to fit into the porphyrin plane (as often suggested). We find the q state lower for a porphyrin hole radius greater than 1.94 A and(More)
We discussed the bonding of O2 to hemoglobin using results of ab initio calculations of idealized portions of the Hb molecule. The bond between Fe and O2 is formed by coupling a triplet state (intermediate spin state) of Fe to the triplet ground state of O2 (analogous to the bonding of O to O2 in ozone). The coordination sphere of the Fe reduces the energy(More)
We present a novel, knowledge-based method for the side-chain addition step in protein structure modeling. The foundation of the method is a conditional probability equation, which specifies the probability that a side-chain will occupy a specific rotamer state, given a set of evidence about the rotamer states adopted by the side-chains at aligned positions(More)
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