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Biomedical subjects

W A Goddard

Publications and source records attributed to W A Goddard.

28 records · Page 2Linked to original sources

Spinons and holons for the one-dimensional three-band Hubbard models of high-temperature superconductors.

The one-dimensional three-band Hubbard Hamiltonian is shown to be equivalent to an effective Hamiltonian that has independent spinon and holon quasiparticle excitations plus a weak coupling of the two. The spinon description includes both copper sites and oxygen hole sites leading to a one-dimensional antiferromagnet incommensurate with the copper lattice. The holons are spinless noninteracting fermions in a simple cosine band. Because the oxygen sites are in the Hamiltonian, the quasiparticles are much simpler than in the exact solution of the t-J model for 2t = +/- J. If a similar description is correct for two dimensions, then the holons will attract in a p-wave potential.

Journal Article↗

Design superiority of palindromic DNA sites for site-specific recognition of proteins: tests using protein stitchery.

Using protein stitchery with appropriate attachment of cysteines linking to either C or N termini of the basic region of the v-Jun leucine zipper gene-regulatory protein, we constructed three dimers--pCC, pCN, and pNN. All three bind specifically to the appropriately rearranged DNA recognition sites for v-Jun: ATGAcgTCAT, ATGAcgATGA, and TCATcgTCAT, respectively (Kd, approximately 4 nM at 4 degrees C). Results of DNase I footprinting provide strong support for bent recognition helices in leucine zipper protein-DNA complexes. Comparison of the results for pCC and pNN with those for pCN shows the design superiority of palindromic sequences for protein recognition.

Amino Acid Sequence↗

Mechanism of superconductivity in K3C60.

Using electronic states and phonon states from the first-principles calculations and including both conventional electron-phonon charge coupling and Jahn-Teller coupling, we predict Tc and other superconducting properties. The only adjustable parameter in the theory is the screening length, Rsc. Using Rsc = 0.8-1.0 A, we find excellent agreement with experiment for Tc (16-18 K), pressure dependence of Tc (Delta Tc = -6 to -10 K for 1 GPa), and 12 C to 13 C isotope shift (alphaC = 0.2); experimental values: 19 K, -7 K, and 0.3, respectively.

Journal Article↗

Protein stitchery: design of a protein for selective binding to a specific DNA sequence.

We present a general strategy for designing proteins to recognize DNA sequences and illustrate this with an example based on the "Y-shaped scissors grip" model for leucine-zipper gene-regulatory proteins. The designed protein is formed from two copies, in tandem, of the basic (DNA binding) region of v-Jun. These copies are coupled through a tripeptide to yield a "dimer" expected to recognize the sequence TCATCGATGA (the v-Jun-v-Jun homodimer recognizes ATGACTCAT). We synthesized the protein and oligonucleotides containing the proposed binding sites and used gel-retardation assays and DNase I footprinting to establish that the dimer binds specifically to the DNA sequence TCATCGATGA but does not bind to the wild-type DNA sequences, nor to oligonucleotides in which the recognition half-site is modified by single-base changes. These results also provide strong support for the Y-shaped scissors grip model for binding of leucine-zipper proteins.

Amino Acid Sequence↗

Superconducting properties of copper oxide high-temperature superconductors.

The equations for the magnon pairing theory of high-temperature copper-oxide-based superconductors are solved and used to calculate several properties, leading to results for specific heat and critical magnetic fields consistent with experimental results. In addition, the theory suggests an explanation of why there are two sets of transition temperatures (T(c) approximately 90 K and T(c) approximately 55 K) for the Y(1)Ba(2)Cu(3)O(6+x) class of superconductors. It also provides an explanation of why La(2-x)Sr(x)CuO(4) is a superconductor for only a small range of x (and suggests an experiment to independently test the theory). These results provide support for the magnon pairing theory of high-temperature superconductors. On the basis of the theory, some suggestions are made for improving these materials.

Journal Article↗

Predictions of structural elements for the binding of Hin recombinase with the hix site of DNA.

Molecular dynamics simulations were coupled with experimental data from biochemistry and genetics to generate a theoretical structure for the binding domain of Hin recombinase complexed with the hix site of DNA. The theoretical model explains the observed sequence specificity of Hin recombinase and leads to a number of testable predictions concerning altered sequence selectivity for various mutants of protein and DNA.

Amino Acid Sequence↗

Theoretical studies of oxygen binding.

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 separation between the quintet, triplet, and singlet states, making an intermediate spin state accessible for bond formation. This provides the mechanism by which an O2 molecule can easily and reversibly bind to Hb. Neither the diamagnetic (t2g) excited state of Fe nor the excited singlet state of O2 play a role in the formation of the FeO2 bond. We also discussed the role of the Fe intra-atomic exchange terms and show how they serve to store electronic energy upon bond formation. An example was given, illustrating how this stored electronic energy can then be used to drive enzymatic reactions. Metal atoms such as ferrous Fe are capable of existing in several distinct electronic configurations, depending upon the ligands. Our objective here has been to illustrate the different characteristics of these Fe configurations and to indicate why various axial ligands stabilize particular Fe configurations. In addition, we have sketched the type of orbital descriptions arising from theoretical wavefunctions and illustrated how to use these descriptions to predict chemical phenomena.

Heme↗

Molecular description of dioxygen bonding in hemoglobin.

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 the t state lower for smaller sizes. For the five-coordinate complex including an axial nitrogenous ligand [a model for myoglobin (Mb) and hemoglobin (Hb)], we find the ground state to be q with the Fe 0.3 A out of the plane (recent x-ray data on deoxy Mb suggests about 0.4 A). The origin of this out-of-plane displacement is the nonbonded repulsions between the axial ligand and porphyrin nitrogen orbitals. Pushing the Fe of the five-coordinate complex into the plane does not lead to a stable low-spin state (as usually suggested), the q and t states being the low-lying states. Bonding the O2 to form the six-coordinate complex stabilizes the t form of the Mb model, leading to a singlet state of MbO2 with Fe in the plane. (It has often been suggested that the Fe of MbO2 and HbO2 is low-spin Fe2+; however, we find this not to be the case.) The bonding in the MbO2 model confirms the ozone model of the bonding, leading to a structure consistent with the Pauling model (our calculated FeOO bond angle is 119 degrees). The total charge transfer to the O2 is 0.10 electron, in disagreement with the Weiss model. Molecular orbital calculations (Hartree-Fock) incorrectly lead to septet ground state (S = 3) for the MbO2 model. The implications for the cooperative O2 binding in hemoglobin and protein modifications of the energetics of the active site are considered. Use of our calculated force constants for displacement of Fe perpendicular to the heme plane suggests that the movement of the Fe upon a change in the quaternary structure from the T to the R form is only about 0.04 A toward the heme plane.

Binding Sites↗

Ozone model for bonding of an O2 to heme in oxyhemoglobin.

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 corroborate this model. Our model is based closely upon the bonding in ozone which recent theoretical studies have shown to be basically a biradical with a singlet state stabilized by a three-center four-electron pi bond. In this model, the facile formation and dissociation of the Fe-O2 bond is easily rationalized since the O2 always retains its triplet ground state character. The ozone model leads naturally to a large negative electric field gradient (in agreement with Mössbauer studies) and to z-polarized (perpendicular to the heme) charge transfer transitions. It also suggests that the 1.3 eV transition, present in HbO2 and absent in HbCO, is due to a porphyrin-to-Fe transition, analogous to that of ferric hemoglobins (e.g., HbCN).

Chemical Phenomena↗