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.     

Nickelocene chemistry : II. New methylidyne trinickel cluster compounds

The new methylidene trinickel cluster complexes, [RCNi₃(η⁵-C₅H₅₃] (R  CMe₃ or SiMe₃) and [Me₃SiCNi₃(η⁵-C₅H₅)2(η⁵-C₅H₄CH₂SiMe₃)] have been isolated in low yield from reactions between nickelocene and the corresponding alkyllithium reagents, RCH₂Li. The compounds [RCNi₃(η⁵-C₅H₅)₃] (R  Ph, CMe₃ or SiMe₃) have also been obtained by treatment of the σ-alkylnickel complexes [(η⁵-C₅H₅)Ni(CH₂R)(PPh₃)] with n-BuLi in the presence of an excess of nickelocene, but under similar conditions [(η⁵-C₅H₅)Ni(CH₂C_1OH₇-2)-(PPh₃)] (where C_1OH₇-2  2-naphthyl) failed to give [2-C_1OH₇CNi₃(η⁵-C₅H₅)₃]. The attempted synthesis of [(η⁵-C₅H₅)Ni(CH₂CCH)(PPh₃)] from [(η⁵-C₅H₅)-NiBr(PPh₃)] and CHCCH₂MgBr gave only [(η⁵-C₅H₅)Ni(CCMe)(PPh₃)] by an unusual rearrangement reaction.     

Quenching echo modulations in NMR spectroscopy.

In NMR spectroscopy, homonuclear scalar couplings normally lead to modulations of spin echoes that tend to interfere with the accurate determination of transverse relaxation rates by Carr-Purcell-Meiboom-Gill (CPMG) multiple refocusing experiments. Surprisingly, the echo modulations are largely cancelled when the refocusing pulses applied to the coupling partner deviate slightly from ideal pi rotations due to tilted effective radio-frequency (RF) fields, even at offsets that are much smaller than the radio-frequency amplitude. Experiments and simulations illustrate these effects for two-spin IS systems containing donor and acceptor (15)N nuclei I=N (D) and S=N(A) in RNA Watson-Crick base pairs with homonuclear scalar couplings J(IS)=(2h)J(N(D), N(A)) across the hydrogen bonds.     

Metamorphosis of ordered mesopores to micropores: periodic silica with unprecedented loading of pendant reactive organic groups transforms to periodic microporous silica with tailorable pore size

Ordered porous silicas with unprecedented loadings of pendant vinyl groups have been synthesized via co-condensation of tetraethyl orthosilicate (TEOS) and triethoxyvinylsilane (TEVS) under basic conditions in the presence of cetyltrimethylammonium surfactant. The resulting organosilicate-surfactant composites exhibited at least one low-angle X-ray diffraction (XRD) peak up to the TEVS:TEOS molar ratio of 7:3 (70% TEVS loading) in the synthesis gel. The surfactant was removed from these composites without any structural collapse. Nitrogen adsorption provided strong evidence of the presence of uniformly sized pores and the lack of phase separation up to TEVS:TEOS ratios as high as 13:7 (65% TEVS loading), whereas (29)Si MAS NMR and high-resolution thermogravimetry showed essentially quantitative incorporation of the organosilane. Thus, a hitherto unachieved loading level for pendant groups, considered by many to be impossible to achieve for stable organosilicas because of the expected framework connectivity constraints, has been obtained. The resulting vinyl-functionalized silicas exhibited gradually decreasing pore diameter (from 2.8 to 1.7 nm for TEVS loadings of 25-65%) and pore volume as the loading of pendant groups increased, but the specific surface area was relatively constant. Because of the reactivity of vinyl groups, ordered silicas with very high loadings of these groups are expected to be robust starting materials for the synthesis of other organic-functionalized ordered microporous materials. Herein, we demonstrate that these starting materials can also be transformed via calcination into ordered microporous silicas with pore diameters tailorable from 2.5 to as little as 1.4 nm simply by using an appropriate loading of the vinyl-functionalized precursor. This ease of the micropore size adjustment and the attained degree of structural ordering (as judged from XRD) have not been reported before. The novel ordered microporous materials reported herein are promising as adsorbents and catalyst supports.     

NMR study of some sydnones,isosydnones, and isothiosydnones

Multinuclear¹H,¹³C,¹⁴N,¹⁵N, and¹⁷O NMR data are presented for some sydnones, isosydnones and isothiosydnones. The type of valence tautomerism shown in (Fig. 1) is not observed for the compounds studied. At high pH compounds2 and12 are found to undergo transformations. The more suitable NMR parameters are reported for establishing the structures of mesoionic compounds containing three heteroatoms in the five-membered conjugated ring. Someab initio GIAO calculations on a model structure of sydnones and related compounds have been performed.     

Synthesis and mass spectrum of 3-(3′-pyridinyloxymethyl)pyridine and polarography of its dialkyl diquaternary salts

3-(3′-Pyridinyloxymethyl)pyridine is prepared by reaction of 3-hydroxymethylpyridine with 3-bromopyridine and converted to the 1,1′-dimethyl and 1,1′-diethyl diquaternary salts with alkyl iodides. The salts are reduced polarographically at a potential (E_o) of about - 1.02 to - 1.10 V in the pH range of 5.5-8.5.