The application of the genetic algorithm to the minimization of potential energy functions

We adapted the genetic algorithm to minimize the AMBER potential energy function. We describe specific recombination and mutation operators for this task. Next we use our algorithm to locate low energy conformation of three polypeptides (AGAGAGAGA, A9, and [Met]-enkephalin) which are probably the global minimum conformations. Our potential energy minima are –94.71, –98.50, and –48.94 kcal/mol respectively. Next, we applied our algorithm to the 46 amino acid protein crambin and located a non-native conformation which had an AMBER potential energy 150 kcal/mol lower than the native conformation. This is not necessarily the global minimum conformation, but it does illustrate problems with the AMBER potential energy function. We believe this occurred because the AMBER potential energy function does not account for hydration.     

Identification of formylglycine in sulfatases by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

C(alpha)-Formylglycine, the catalytic amino acid residue in the active site of sulfatases, is generated by post-translational modification of a cysteine or serine residue. We describe a highly sensitive procedure for the detection of C(alpha)-formylglycine-containing peptides in tryptic digests of sulfatase proteins. The protocol is based on the formation of hydrazone derivatives of C(alpha)-formylglycine-containing peptides when using dinitrophenylhydrazine as a matrix for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). The hydrazone derivatives desorb and ionize with high efficiency and can be detected in the sub-femtomole range. The presence of C(alpha)-formylglycine is indicated by a mass increment of 180.13 u, corresponding to the hydrazone moiety, and also by a unique C-terminal fragment ion, characteristic of sulfatases, that becomes prominent in MALDI post-source decay mass spectra of the hydrazone derivatives.     

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.     

Evaluation of recombinant green fluorescent protein, under various culture conditions and purification with HiTrap hydrophobic interaction chromatography resins

To determine the influence of various culture conditions, transformed cells of Escherichia coli expressing recombinant green fluorescent protein (GFPuv) were grown in nine cultures with four variable conditions (storage of inoculated broth at 4°C prior to incubation, agitation speed, isopropyl-β-d-thiogalactopyranoside [IPTG] concentration, and induction time). The pelleted cells were resuspended in extraction buffer and subjected to the three-phase partitioning (TPP) extraction method. To determine the most appropriate purification resin, protein extracts were eluted through one of four types of HiTrap hydrophobic interaction chromatography (HIC) columns prepacked with methyl, butyl, octyl, or phenyl resins and analyzed further on a 12% sodium dodecylsulfatepolyacrylamidegel. With Coomassie staining, a single band between 27 (standard GFPuv) and 29 kDa (molecular weight standard) was visualized for every HIC column sample. TPP extraction with HIC elution provided about 90% of the GFPuv recovered and eight-fold GFPuv enrichment related to the specific mass. Rotary speed and IPTG concentration showed, respectively, greater negative and positive influences on GFPuv expression at the beginning of the logarithmic phase for the set culture conditions (37°C, 24-h incubation).     

Activation of trisacryl gels with chloroformates and their use for affinity chromatography and protein immobilization

In this study we describe the activation with chloroformates of Trisacryl-GF-2000, a new synthetic gel support that is stable, hydrophilic, and contains large amounts of hydroxyl groups available for activation. Of all the reagents tested, the activation withN-hydroxysuccinimide-chloroformate andp-nitrophenylchloroformate in organic solvents provides the best activation yield and subsequent coupling. When Trisacryl was activated in acetone with the chloroformates in the presence of 4-dimethylaminopyridine as base and catalyst, up to 30% of the hydroxyl groups, (i.e., 1/repeating unit) could be activated. Amino-containing ligands and proteins could be coupled to these carriers at pH 8 or higher. For better results in affinitychromatographic applications, spacers of ε-amino caproic acid or diaminohexane were introduced. The efficacy of these columns was demonstrated by purification of enzymes, antibodies, and antigens. The performance of these new columns were compared with that of Sepharose columns activated in various ways. In every case, the properties of the Trisacryl support proved superior with particular reference to the purity of the product obtained.     

Molecular Replacement Studies of Cucurmosin from Cucurbita Moschata:Structure Homology with Trichosanthin

1 INTRODUCTION Many plants contain proteins that are capable of inactivating ribosomes and therefore are called ribosome-inactivating proteins or RIPs[1]. RIPs are RNA N-glycosidases that inactivate ribosomes through a site-specific deadenylation of the large ribosomal RNA[2, 3]. RIPs are also capable of inactivating many nonribosomal nucleic acid substrates and can be considered as polynucleotide: adenosine glycosidases[4～6]. There are two types of RIPs: type I, single chain pr…     

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.     

Photoinitiators with functional groups. V. New water‐soluble photoinitiators containing carbohydrate residues and copolymerizable derivatives thereof

The synthesis of new water‐soluble photoinitiators (PIs) based on hydroxyalkylphenones, benzophenones, and thioxanthones with carbohydrate residues such as glucose, cellobiose, and 1‐amino‐1‐deoxy‐D ‐glucitol (glucamine) is described. In addition, selected initiators were reacted with methacryloyl chloride to obtain copolymerizable initiators with improved migration stability. Results from photo differential scanning calorimetry and gel‐content measurements in commercially available water‐thinnable and emulsion‐type resins as well as 2‐hydroxyethyl acrylate are included. Glucose‐modified PIs gave the best results with respect to compatibility with the resin, reactivity, and gel content. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1504–1518, 2002     

Synthesis and properties of segmented aromatic poly(ether sulfone)-amide and poly(ether sulfone)-imide copolymers

New segmented aromatic poly(ether sulfone)-amide and poly(ether sulfone)-imide copolymers were synthesized by the chain extension of α,w-diamine-terminated poly(ether sulfone) oligomer with both aromatic dicarboxylic acid chlorides and tetracarboxylic dianhydrides, respectively. Crystallization of the poly(ether sulfone)unit was suppressed by the introduction of amide or imide linkage along the polymer backbone, giving amorphous copolymers that were +eadily soluble in various organic solvents. The copolymers had somewhat higher glass transition temperatures than the parent poly(ether sulfone). They afforded transparent and tough films by solution casting. © 1992 John Wiley & Sons, Inc.     

Purification of recombinant green fluorescent protein by three-phase partitioning

The technique of three-phase partitioning (TPP) was used to purify the green fluorescent protein (GFP) in a single step. TPP uses a combination of ammonium sulphate and tert-butanol to precipitate proteins from their crude extracts. In the first round of TPP with 20% ammonium sulphate saturation at the ratio of crude to tert-butanol 1:1 (v/v), most of the GFP remains in the lower aqueous phase. When subjected to a second round of TPP with 60% ammonium sulphate saturation at the ratio of crude to tert-butanol 1:2 (v/v) gives 78% recovery of GFP with a 20-fold purification. The sodium dodecyl sulphate-polyacrylamide gel electrophoretic (SDS-PAGE) analysis of purified preparation shows single band. The fluorescence excitation and emission spectra agreed with values reported in literature.