Analysis of the stabilization of hen lysozyme by helix macrodipole and charged side chain interaction

In the N-terminal region of the alpha-helix of the c-type lysozymes, two Asx residues exist at the 18th and 27th positions. Hen lysozyme has Asp18/Asn27 (18D/27N), and we prepared three mutant lysozymes, Asn18/Asn27 (18N/27N), Asn18/Asp27 (18N/27D), and Asp18/Asp27 (18D/27D). The stability of the wild-type (18D/27N) lysozyme supported the existence of a hydrogen bond between the side chain of Asp18 and the amide group at the N1 position in the alpha-helix, while the stability of the 18N/27D lysozyme supported the presence of the capping box between the Ser24 (N-cap) and Asp27 residues. Although electrostatic repulsion was observed between Asp18 and Asp27 residues in 18D/27D lysozyme, the dissociation of each residue contributed to stabilizing the B-helix in 18D/27D lysozyme through hydrogen bonding and charge-helix macrodipole interaction. This is the first evidence that two neighboring negative charges at the N-terminus of the helix both increased the stability of the protein.     

Insights into transition state stabilization of the beta-1,4-glycosidase Cex by covalent intermediate accumulation in active site mutants

The catalytic mechanism of 'retaining' beta-glycosidases has been the subject of considerable interest and debate for many years. The visualization of a covalent glycosyl enzyme intermediate by X-ray crystallography was first accomplished with a saccharide substrate substituted with fluorine at its 2-position. The structure implicated major roles for residue His 205 and for the 2-hydroxyl position of the proximal saccharide in binding and catalysis. Here we have studied the kinetic behavior of various His 205 mutants. One of these mutants, a double mutant H205N/E127A, has been used to stabilize a covalent glycosyl-enzyme intermediate involving an unsubstituted sugar, permitting crystallographic analysis of the interactions between its 2-hydroxyl group and the enzyme.     

Practical synthesis of Taxol side chain

Practical large scale synthesis of N-benzoyl-(2R,3S)-phenylisoserine methyl ester of the Taxol side chain has been attained from the coupling of chiral imine of N-[(S)-methylbenzyl]benzaldimine with (Z)-alpha-methoxy trimethylsilyl ketene acetal followed by the sequential reactions of lactamization, demethylation, methanolysis and N-benzoylation.     

Proton selective substate of the mitochondrial permeability transition pore: regulation by the redox state of the electron transport chain

The permeability transition pore of rat liver mitochondria can be closed by chelating free Ca2+, with respect to the passage of large molecules such as mannitol and sucrose. However, an apparent H+-conducting substate remains open under these conditions, as indicated by the persistence of maximal O2 consumption rates and by the failure to recover a membrane potential. Agents which favor a closed pore, such as cyclosporin A, ADP, Mg2+, or bovine serum albumin, do not close the H+-conducting substate, but it closes spontaneously when respiration becomes limited by the availability of O2. Closure provoked by an O2 limitation requires free Mg2+ in the sub-micromolar concentration range and becomes less efficient with increasing time spent in the presence of free Ca2+. The H+-conducting substate is apparently regulated by the redox status of the electron transport chain, with a reduced form favoring closure. A physical association (or equivalence) between the pore and one of the respiratory chain complexes is supported. These characteristics suggest that the transition is irreversible in vivo, if it involves a small fraction of total mitochondria, and would lead to their elimination and/or replacement by the cell. The implications of this proposal are considered, as they relate to a possible role for the transition in cellular apoptosis and the elimination of mitochondria containing mutated DNA.     

Active serine involved in the stabilization of the active site loop in the Humicola lanuginosa lipase

We have investigated the binding properties of and dynamics in Humicola lanuginosa lipase (Hll) and the inactive mutant S146A (active Ser146 substituted with Ala) using fluorescence spectroscopy and molecular dynamics simulations, respectively. Hll and S146A show significantly different binding behavior for phosphatidylcholine (PC) and phosphatidylglycerol (PG) liposomes. Generally, higher binding affinity is observed for Hll than the S146A mutant. Furthermore, depending on the matrix, the addition of the transition state analogue benzene boronic acid increases the binding affinity of S146A, whereas only small changes are observed for Hll suggesting that the active site lid in the latter opens more easily and hence more lipase molecules are bound to the liposomes. These observations are in agreement with molecular dynamics simulations and subsequent essential dynamics analyses. The results reveal that the hinges of the active site lid are more flexible in the wild-type Hll than in S146A. In contrast, larger fluctuations are observed in the middle region of the active site loop in S146A than in Hll. These findings reveal that the single mutation (S146A) of the active site serine leads to substantial conformational alterations in the H. lanuginosa lipase and different binding affinities.     

The enethiolate anion reaction products of EpiD. Pka value of the enethiol side chain is lower than that of the thiol side chain of peptides

One of the steps involved in the biosynthesis of the lantibiotic epidermin is the oxidative decarboxylation reaction of peptides catalyzed by the flavoenzyme EpiD. EpiD catalyzes the formation of a (Z)-enethiol derivative from the C-terminal cysteine residue of the precursor peptide of epidermin and related peptides. The UV-visible spectra of the reaction products of EpiD are pH-dependent, indicating that the enethiol side chain is converted to an enethiolate anion. The pKa value of the enethiol group was determined to be 6.0 and is substantially lower than the pKa value of the thiol side chain of cysteine residues. The increased acid strength of the enethiol side chain compared with that of the thiol group is attributed to the resonance stabilization of the negative charge of the anion.     

Ab initio conformational study of the phenylisoserine side chain of paclitaxel

Paclitaxel (Taxol) and related compounds are important antitumor drugs, currently used for the treatment of several types of cancer. The flexible amino acidic C13 side chain is a key element of the taxoid pharmacophore, and the identification of the bioactive conformation is a top priority for a better understanding of the mode of action of these anticancer agents. The conformational features of the side chain have been investigated by Hartree-Fock ab initio and semiempirical PM3 calculations. To gain a better understanding of solvent effects, different molecular models of paclitaxel were used in the calculations. The gas-phase calculations confirm that only one conformation, named ch1 (very similar to the one found in the crystal structure of docetaxel), is present in apolar environments. The preference for this conformer has been rationalized in terms of its L shape, which minimizes steric and Coulombic interactions, and of a favorable arrangement of the glycolate moiety. When a polar solvent was simulated by different methods, a greater conformational variability was found, with different conformations differing by less than 1.5 kcal/mol. Among these conformations, only one (ch5', similar to molecule B of the crystal structure of paclitaxel) is particularly apt to interact with solvent molecules. In light of these data, it seems reasonable to assume that, when the drug is bound to the lipophilic pocket of the tubuline receptor, the C13 amino acidic side chain assumes a conformation close to ch1.     

Determinants of side chain conformational preferences in protein structures

A discriminatory function based on a statistical analysis of atomic contacts in protein structures is used for selecting side chain rotamers given a peptide main chain. The function allows us to rank different possible side chain conformations on the basis of contacts between side chain atoms and atoms in the environment. We compare the differences in constructing side chain conformations using contacts with only the local main chain, using the entire main chain, and by building pairs of side chains simultaneously with local main chain information. Using only the local main chain allows us to construct side chains with approximately 75% of the chi1 angles within 30 degrees of the experimental value, and an average side chain atom r.m.s.d. of 1.72 A in a set of 10 proteins. The results of constructing side chains for the 10 proteins are compared with the results of other side chain building methods previously published. The comparison shows similar accuracies. An advantage of the present method is that it can be used to select a small number of likely side chain conformations for each residue, thus permitting limited combinatorial searches for building multiple protein side chains simultaneously.     

Identification of genes controlling the transition of Salmonella typhimurium bacteria to a non-culturable state

Mutants of Salmonella typhimurium with an impaired process of transition to the nonculturable state were tainted. Mutants were divided into four phenotypic groups. In four mutants (representatives of each phenotypic group), genes with TnPhoA transposon insertions were cloned; these insertions caused a disturbance in the process of mutant cell transition to the nonculturable state. Nucleotide sequences of mutant gene fragments were determined. Comparison of nucleotide sequences obtained with a data bank on DNA nucleotide sequences of enterobacterial genomes allowed the identification of four genes involved in the control of nonculturable form generation in salmonellae.     

Site-directed mutagenesis of active site contact residues in a hydrolytic abzyme: evidence for an essential histidine involved in transition state stabilization

Specific molecular interactions involved in catalysis by antibody 6D9 were investigated by site-directed mutagenesis. The catalytic antibody 6D9, which was generated against a transition state analog (III), hydrolyzes a non-bioactive chloramphenicol monoester derivative (I) to produce chloramphenicol (II). Construction of a three-dimensional molecular model of 6D9 and sequence comparison within a panel of related antibodies suggested candidates for catalytic residues, His (L27d), Tyr (L32), Tyr (H58) and Arg (H100b); these were targeted for the site-directed mutagenesis study. The Y-H58-F and R-H100b-A mutants possessed catalytic activities comparable to that of the wild-type, and the Y-H58-H and Y-L32-F mutant displayed an approximately fivefold decrease in k(cat)/Km. In the transition state analysis, the plots of logK(TSA) versus log(k(cat)/Km) for the mutants are linear, with a slope of approximately 1.0, indicating that the entire hapten-binding energy in the mutants is also utilized to bind the transition state and to accelerate the catalysis. In addition, a dramatic change in the catalytic activity was observed when the histidine residue (27d) in the CDR1 light chain was replaced with alanine. The H-L27d-A mutant had no detectable catalytic activity. This mutation led to a large, 40-fold reduction in transition state binding, with no change in substrate binding. Coupled with the previous kinetic studies and chemical modifications of the intact 6D9 antibody, this mutagenesis study has demonstrated that His L27d plays an essential role in stabilization of the transition state, the mechanism of catalysis by the 6D9 antibody.     

Evidence for stabilization of the low-spin state of cytochrome P450 due to shortening of the proximal heme bond

The cytochrome P450 superfamily of enzymes is ubiquitous, being responsible for the metabolism of a wide range of endogenous and xenobiotic compounds. However, the detailed mechanism of the catalytic cycle of these enzymes is still not fully understood. We describe results, obtained from first principles molecular simulations, which indicate that the low-spin state of the Fe3+ ion, present in the heme moiety at the active site of a cytochrome P450 enzyme, may be stabilized by shortening of the proximal bond of the heme. Calculations indicate that a bond length of less than approximately 2.05 A between the heme Fe3+ ion and the cysteine S, which forms the proximal ligand, would result in the stabilization of the low-spin state of the Fe3+, inhibiting the progress of the P450 catalytic cycle. Our investigation uses novel first principles modeling techniques which treat the entire system quantum-mechanically.     

Boundaries of the single-phase side fields of the system Mo-Cu-Ni in the solid state

Conclusions It was established that the molybdenum corner of the Mo-Cu-Ni ternary system contains a singlephase field of solid solutions of copper and nickel in molybdenum with a combined Cu and Ni content of 1.5–2 wt.%. At the copper-nickel side of the constitution diagram of this system, there is a single-phase field of ternary Cu-Ni-Mo solid solutions, whose molybdenum content steadily rises with increase in nickel concentration, from 1.5 wt.% at NiCu=2080 to 3 wt.% at NiCu=4060.Translated from Poroshkovaya Metallurgiya, No. 2 (122), pp. 65–70, February, 1973.     

Approaching the transition state in the crystal structure of a phosphoribosyltransferase

Hypoxanthine phosphoribosyltransferase (HPRT) salvages 6-oxopurine bases in the nucleotide metabolic pathway. The 1.8 A crystal structure of an asymmetric dimer of the HPRT from the protozoan parasite Trypanosoma cruzi was determined in a ternary complex with the primary substrate phosphoribosylpyrophosphate (PRPP) and an analogue of the substrate hypoxanthine, revealing both open and closed active site conformations. The ligands are positioned for in-line nucleophilic attack at the PRPP ribose C1' by two metal ions which straddle the pyrophosphate leaving group. The structure provides the first evidence for the involvement of two metal ions in the HPRT-catalyzed reaction, and structural details further suggest the mechanism may proceed via SN2-type chemistry. The closed conformation reveals the structural roles for invariant flexible loop residues Ser103 and Tyr104 and supports a role for the loop in the liberation of pyrophosphate. The pre-transition state structure is valuable for understanding the enzyme mechanism, as well as providing a foundation for antiparasite drug design efforts against T. cruzi, which causes Chagas' disease in humans. Additionally, the structure illuminates the molecular basis of three inherited mutations in the human HPRT leading to Lesch-Nyhan syndrome (D193N) or gout (S103R or S109L), as the homologous residues in the trypanosomal enzyme contribute to the previously unrecognized Mg2+ ion binding site and to the formation of the closed flexible loop, respectively.     

Guidelines for protein design: the energetics of beta sheet side chain interactions

To determine the interaction energy between cross-strand pairs of side chains on an antiparallel beta sheet, pairwise amino acid substitutions were made on the solvent-exposed face of the B1 domain of streptococcal protein G. The measured interaction energies were substantial (1.8 kilocalories per mole) and comparable to the magnitude of the beta sheet propensities. The experimental results paralleled the statistical frequency with which the residue pairs are found in beta sheets of known structure.     

Change in environment of the P1 side chain upon progression from the Michaelis complex to the covalent serpin-proteinase complex

Serpins inhibit proteinases by forming a kinetically trapped intermediate during a suicide substrate inhibition reaction. To determine whether the kinetic trap involves a repositioning of the P1 side chain of the serpin following formation of the initial Michaelis complex, we used the tryptophan of a P1 M-->W variant of human alpha1-proteinase inhibitor as a fluorescent reporter group of the environment of the P1 side chain. The P1W variant was a valid model serpin and formed SDS-stable complexes with both trypsin and chymotrypsin with a stoichiometry of inhibition close to 1.0. Rates of inhibition of chymotrypsin for wild-type and variant alpha1-proteinase inhibitor differred only approximately 1.8-fold. Rates of inhibition of trypsin were, however, 25-fold lower for the variant than for the wild-type inhibitor. Steady-state fluorescence spectra showed a change in environment for the P1 side chain upon forming both covalent complex with trypsin or chymotrypsin and noncovalent complex with anhydrochymotrypsin. The P1 environments in the chymotrypsin and anhydrochymotrypsin complexes were, however, different. Fluorescence quenching studies confirmed the burial of the P1 side chain upon formation of both the noncovalent and covalent complexes, but were not able to discriminate between the solvent accessibility in these complexes. Stopped-flow fluorescence measurements resolved the covalent intramolecular reaction that led to covalent complex and showed that, during the course of the covalent reaction, the environment of the P1 side chain changed consistent with a repositioning relative to residues of the proteinase active site as part of formation of the trap. This repositioning is likely to be a crucial part of the trapping mechanism.