Measurement of long-range cross-correlation rates using a combination of single- and multiple-quantum NMR spectroscopy in one experiment

A method is described to determine long-range cross-correlations between the modulations of an anisotropic chemical shift (e.g., of a C' carbonyl carbon in a protein) and the fluctuations of a weak long-range dipolar interaction (e.g., in cross-correlation between the same C' carbonyl and the H(N) proton of the neighboring amide group). Such long-range correlations are difficult to measure because the corresponding long-range scalar couplings are so small that Redfield's secular approximation is often violated. The method, which combines features of single- and double-quantum NMR spectroscopy, allows one to cancel the effects of dominant short-range dipolar interactions (e.g., between the CSA of the amide nitrogen N and the dipolar coupling to its attached proton H(N)) and is designed so that the secular approximation is rescued even if the scalar coupling between the long-range dipolar coupling partners is very small. The cross-correlation rates thus determined in ubiquitin cover a wide range because of local motions and variations of the CSA tensors.     

Heteronuclear solid-state correlation spectroscopy

Two-dimensional NMR methods are proposed for correlating the spectra of abundant and dilute spins in solids. The techniques simplify assignment and permit determination of shielding tensors even when extensive overlaps occur. Spin diffusion among abundant spins can be observed indirectly.     

DNA polymerase template interactions probed by degenerate isosteric nucleobase analogs

The development of novel artificial nucleobases and detailed X-ray crystal structures for primer/template/DNA polymerase complexes provide opportunities to assess DNA-protein interactions that dictate specificity. Recent results have shown that base pair shape recognition in the context of DNA polymerase must be considered a significant component. The isosteric azole carboxamide nucleobases (compounds 1-5; ) differ only in the number and placement of nitrogen atoms within a common shape and therefore present unique electronic distributions that are shown to dictate the selectivity of template-directed nucleotide incorporation by DNA polymerases. The results demonstrate how nucleoside triphosphate substrate selection by DNA polymerase is a complex phenomenon involving electrostatic interactions in addition to hydrogen bonding and shape recognition. These azole nucleobase analogs offer unique molecular tools for probing nonbonded interactions dictating substrate selection and fidelity of DNA polymerases.     

Synthesis and characterization of carbohydrate-based phospholipids

Novel carbohydrate-based phospholipids containing two saturated C(12) (dilauroyl ribo-phosphocholine) (DLRPC), C(14) (dimyristoyl ribo-phosphocholine) (DMRPC), and C(20) (diarachadonyl ribo-phosphocholine) (DARPC) carboxylic acid chains were synthesized. The physical properties of the supramolecular structures formed by these compounds were compared to those formed by their direct glycerol analogues dilauroyl phosphocholine (DLPC), dimyristoyl phosphocholine (DMPC), and diarachadonyl phosphocholine (DAPC). Modulated differential scanning calorimetry (MDSC) and X-ray diffraction data indicated that with chain lengths < or =14 carbons, the carbohydrate backbone increased the thermal stability of the bilayer below the phase-transition temperature (T(m)) as compared to the glycerol-based lipids. With longer chains (C(20)), the bilayer structure was destabilized as compared to glycerol-based lipids. NMR studies of a DMRPC vesicle dispersion reveal split choline headgroup signals and distinct magnetization transfer effects arising from the "inner" and "outer" surfaces of the bilayer vesicle. Modulated differential scanning calorimetry also demonstrated that glycerol- and carbohydrate-based lipids mix, as evidenced by a single intermediate T(m). In addition, carbohydrate-based lipid/cholesterol mixtures exhibited a decrease in enthalpy with an increase in cholesterol concentration. Unlike glycerol phospholipids, carbohydrate lipids were resistant to enzymatic degradation by phospholipase A(2) (PLA(2)).     

THE MOLECULAR WEIGHT OF HAEMATOPORPHYRIN DERIVATIVE, ITS GEL COLUMN FRACTIONS and SOME OF ITS COMPONENTS IN AQUEOUS SOLUTION

Abstract— The average molecular weights of haematoporphyrin derivative (HPD), the fractions of HPD that can he obtained by gel chromatography and of purified haematoporphyrin and protoporphyrin in aqueous solution have been determined by ultracentrifugation. The results show that HPD contains polymeric material with the excluded fraction from the gel column (HPD aggregate) having an average molecular weight of greater than 20000. The two remaining gel column fractions of HPD have lower molecular weights and their similarity indicates that these fractions do not separate because of molecular weight differences. Purified haematoporphyrin has a comparatively low molecular weight in aqueous solution but the data is not capable of discriminating between monomer, dimer or slightly higher oligomer. In contrast, protoporphyrin sediments to the bottom of the centrifuge tube under the conditions of sedimentation equilibrium indicating that it has an average molecular weight considerably greater than that of HPD aggregate.     

Nonabelian orbifolds and the boson-fermion correspondence

For a positive integerl divisible by 8 there is a (bosonic) holomorphic vertex operator algebra (VOA) associated to the spin lattice _l . For a broad class of finite groupsG of automorphisms of we prove the existence and uniqueness of irreducibleg-twisted -modules and establish the modular-invariance of the partition functionsZ(g, h, ) for commuting elements inG. In particular, for any finite group there are infinitely many holomorphic VOAs admittingG for which these properties hold. The proof is facilitated by a boson-fermion correspondence which gives a VOA isomorphism between and a certain fermionic construction, and which extends work of Frenkel and others.Supported by NSA grant MDA904-92-H-3099.Supported by NSF grant DMS-9122030.     

High-Valent Manganese in Polyoxotungstates. 3. Dimanganese Complexes of gamma-Keggin Anions

Dimanganese-substituted gamma-Keggin heteropoly tungstates have been synthesized by reaction of the lacunary species gamma-[(SiO(4))W(10)O(32)](8)(-) with appropriate mixtures of Mn(II) and MnO(4)(-). The crystal structure of [(CH(3))(3)(C(6)H(5))N](4)[(SiO(4))W(10)Mn(III)(2)O(36)H(6)].2CH(3)CN.H(2)O (anion 1) was determined by X-ray diffraction. Crystallographic data: space group P&onemacr;, a = 12.951(3) ?, b = 14.429(3) ?, c = 20.347(4) ?, alpha = 81.95(3) degrees, beta = 88.92(3) degrees, gamma = 67.48(3) degrees, V = 3475.2(13) ?(3), and Z = 2. The final R value is 7.29% for 15861 reflections with I > 2sigma(I). The anion has the anticipated gamma-Keggin structure with virtual C(2)(v)() symmetry. The two Mn cations occupy adjacent, edge-shared octahedra with bridging hydroxo and terminal aqua ligands. Anion 1 can be oxidized and reduced to the corresponding Mn(III)Mn(IV) (2) and Mn(II)(2) (3) species respectively. The magnetic susceptibility of 1 between 2 and 300 K indicates that the Mn(III) cations are antiferromagnetically coupled, with J = -17.0 cm(-)(1) and g = 1.965. No simple magnetic behavior was observed for 2 or 3.     

Preprocessing of rotamers for protein design calculations

We have developed a process that significantly reduces the number of rotamers in computational protein design calculations. This process, which we call Vegas, results in dramatic computational performance increases when used with algorithms based on the dead-end elimination (DEE) theorem. Vegas estimates the energy of each rotamer at each position by fixing each rotamer in turn and utilizing various search algorithms to optimize the remaining positions. Algorithms used for this context specific optimization can include Monte Carlo, self-consistent mean field, and the evaluation of an expression that generates a lower bound energy for the fixed rotamer. Rotamers with energies above a user-defined cutoff value are eliminated. We found that using Vegas to preprocess rotamers significantly reduced the calculation time of subsequent DEE-based algorithms while retaining the global minimum energy conformation. For a full boundary design of a 51 amino acid fragment of engrailed homeodomain, the total calculation time was reduced by 12-fold.     

Exact rotamer optimization for protein design

Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to perform previously intractable designs of entire protein core, surface, or boundary regions. Computational demonstrations include a full core design of the variable domains of the light and heavy chains of catalytic antibody 48G7 FAB with 74 residues and 10(128) conformations, a full core/boundary design of the beta1 domain of protein G with 25 residues and 10(53) conformations, and a full surface design of the beta1 domain of protein G with 27 residues and 10(60) conformations. In addition, a full sequence design of the beta1 domain of protein G is used to demonstrate the strong dependence of algorithm performance on the exact form of the potential function and the fidelity of the rotamer library. These results emphasize that search algorithm performance for protein design can only be meaningfully evaluated on physical models that have been subjected to experimental scrutiny. The new algorithm greatly facilitates ongoing efforts to engineer increasingly complex protein features.     

Computer-aided identification of powdered vegetable materials

The use and limitations of the microcomputer as an aid for the analyst in the identification of powdered vegetable materials is presented and suggestions are given for extending the applicability of the method and the programs described.