Multiple mutations in RNA polymerase ß-subunit gene (rpoB) in Streptomyces incarnatus NRRL8089 enhance production of antiviral antibiotic sinefungin: modeling rif cluster region by density functional theory.

Streptomyces incarnatus NRRL8089 produces the antiviral, antifungal, antiprotozoal nucleoside antibiotic sinefungin. To enhance sinefungin production, multiple mutations were introduced to the rpoB gene encoding RNA polymerase (RNAP) ß-subunit at the target residues, D447, S453, H457, and R460. Sparse regression analysis using elastic-net lasso-ridge penalties on previously reported H457X mutations identified a numeric parameter set, which suggested that H457R/Y/F may cause production enhancement. H457R/R460C mutation successfully enhanced the sinefungin production by 3-fold, while other groups of mutations, such as D447G/R460C or D447G/H457Y, made moderate or even negative effects. To identify why the rif cluster residues have diverse effects on sinefungin production, an RNAP/DNA/mRNA complex model was constructed by homology modeling and molecular dynamics simulation. The 4 residues were located near the mRNA strand. Density functional theory-based calculation suggested that D447, H457, and R460 are in direct contact with ribonucleotide, and partially positive charges are induced by negatively charged chain of mRNA.

Molecular Power Spring: Circular Dichroism Inversion of Polythiophene Aggregates from the Right-Handed Helix to Left-Handed Helix.

In molecular rotors, a type of molecular machine, spontaneous rotors without the need for an external stimulus are promising because conventional molecular rotors require a continuous energy supply. In this study, we demonstrate spontaneous transformation from kinetically favored metastable right-handed helical aggregates to thermodynamically stable left-handed helical aggregates after an evaporation procedure. In addition, we propose the conditions for preparation of metastable right-handed helical aggregates, whose chirality can be spontaneously inverted, based on kinetic analysis. This molecular power spring will be useful for designing new types of molecular machines.

Molecular evolution of gas cavity in [NiFeSe] hydrogenases resurrected in silico.

Oxygen tolerance of selenium-containing [NiFeSe] hydrogenases (Hases) is attributable to the high reducing power of the selenocysteine residue, which sustains the bimetallic Ni-Fe catalytic center in the large subunit. Genes encoding [NiFeSe] Hases are inherited by few sulphate-reducing δ-proteobacteria globally distributed under various anoxic conditions. Ancestral sequences of [NiFeSe] Hases were elucidated and their three-dimensional structures were recreated in silico using homology modelling and molecular dynamic simulation, which suggested that deep gas channels gradually developed in [NiFeSe] Hases under absolute anaerobic conditions, whereas the enzyme remained as a sealed edifice under environmental conditions of a higher oxygen exposure risk. The development of a gas cavity appears to be driven by non-synonymous mutations, which cause subtle conformational changes locally and distantly, even including highly conserved sequence regions.

A third-generation density-functional-theory-based method for calculating canonical molecular orbitals of large molecules.

We used grid-free modified Cholesky decomposition (CD) to develop a density-functional-theory (DFT)-based method for calculating the canonical molecular orbitals (CMOs) of large molecules. Our method can be used to calculate standard CMOs, analytically compute exchange-correlation terms, and maximise the capacity of next-generation supercomputers. Cholesky vectors were first analytically downscaled using low-rank pivoted CD and CD with adaptive metric (CDAM). The obtained Cholesky vectors were distributed and stored on each computer node in a parallel computer, and the Coulomb, Fock exchange, and pure exchange-correlation terms were calculated by multiplying the Cholesky vectors without evaluating molecular integrals in self-consistent field iterations. Our method enables DFT and massively distributed memory parallel computers to be used in order to very efficiently calculate the CMOs of large molecules.

Synthesis and characterization of ethylbis(2-pyridylethyl)amineruthenium complexes and two different types of C-H bond cleavage at an ethylene arm.

Ruthenium complexes bearing ethylbis(2-pyridylethyl)amine (ebpea), which has flexible -C(2)H(4)- arms between the amine and the pyridyl groups and coordinates to a metal center in facial and meridional modes, have been synthesized and characterized. Three trichloro complexes, fac-[Ru(III)Cl(3)(ebpea)] (fac-[1]), mer-[Ru(III)Cl(3)(ebpea)] (mer-[1]), and mer-[Ru(II)Cl(3){η(2)-N(C(2)H(5))(C(2)H(4)py)═CH-CH(2)py}] (mer-[2]), were synthesized using the Ru blue solution. Formation of mer-[2] proceeded via a C-H activation of the CH(2) group next to the amine nitrogen atom of the ethylene arm. Reduction reactions of fac- and mer-[1] afforded a triacetonitrile complex mer-[Ru(II)(CH(3)CN)(3)(ebpea)](PF(6))(2) (mer-[3](PF(6))(2)). Five nitrosyl complexes fac-[RuX(2)(NO)(ebpea)]PF(6) (X = Cl for fac-[4]PF(6); X = ONO(2) for fac-[5]PF(6)) and mer-[RuXY(NO)(ebpea)]PF(6) (X = Cl, Y = Cl for mer-[4]PF(6); X = Cl, Y = CH(3)O for mer-[6]PF(6); X = Cl, Y = OH for mer-[7]PF(6)) were synthesized and characterized by X-ray crystallography. A reaction of mer-[2] in H(2)O-C(2)H(5)OH at room temperature afforded mer-[1]. Oxidation of C(2)H(5)OH in H(2)O-C(2)H(5)OH and i-C(3)H(7)OH in H(2)O-i-C(3)H(7)OH to acetaldehyde and acetone by mer-[2] under stirring at room temperature occurred with formation of mer-[1]. Alternative C-H activation of the CH(2) group occurred next to the pyridyl group, and formation of a C-N bond between the CH moiety and the nitrosyl ligand afforded a nitroso complex [Ru(II)(N(3))(2){N(O)CH(py)CH(2)N(C(2)H(5))C(2)H(4)py}] ([8]) in reactions of nitrosyl complexes with sodium azide in methanol, and reaction of [8] with hydrochloric acid afforded a corresponding chloronitroso complex [Ru(II)Cl(2){N(O)CH(py)CH(2)N(C(2)H(5))C(2)H(4)py}] ([9]).

Study of the quasicanonical localized orbital method based on protein structures.

An initial guess is one of the most important factors in solving self-consistent field (SCF) molecular orbital calculations for large molecules. Recently, the authors reported that the quasicanonical localized orbital (QCLO) method was useful to prove the initial guess for all-electron calculations for proteins. This paper describes a new QCLO method that takes into account protein information derived from protein structures such as salt bridges and the secondary structure of the molecule. In several test calculations using typical models, the difference between the initial guess and final atomic charges was markedly decreased, and the number of SCF iterations was reduced. We suggest that the structure-based QCLO method improves the precision of the initial guess and achievement of automatic all-electron calculations for proteins.

Development of parallel density functional program using distributed matrix to calculate all-electron canonical wavefunction of large molecules.

We developed a new parallel density-functional canonical molecular-orbital program for large molecules based on the resolution of the identity method. In this study, all huge matrices were decomposed and saved to the distributed local memory. The routines of the analytical molecular integrals and numerical integrals of the exchange-correlation terms were parallelized using the single program multiple data method. A conventional linear algebra matrix library, ScaLAPACK, was used for matrix operations, such as diagonalization, multiplication, and inversion. Anderson's mixing method was adopted to accelerate the self-consistent field (SCF) convergence. Using this program, we calculated the canonical wavefunctions of a 306-residue protein, insulin hexamer (26,790 orbitals), and a 133-residue protein, interleukin (11,909 orbitals) by the direct-SCF method. In regard to insulin hexamer, the total parallelization efficiency of the first SCF iteration was estimated to be 82% using 64 Itanium 2 processors connected at 3.2 GB/s (SGI Altix3700), and the calculation successfully converged at the 17-th SCF iteration. By adopting the update method, the computational time of the first and the final SCF loops was 229 min and 156 min, respectively. The whole computational time including the calculation before the SCF loop was 2 days and 17 h. This study put the calculations of the canonical wavefunction of 30,000 orbitals to practical use.

Laparoscopic partial versus total adrenalectomy for aldosterone producing adenoma.

PURPOSE: Laparoscopic surgery has become a standard method for adrenal treatment. Primary hyperaldosteronism is known to be frequently characterized by multiple adrenal lesions. The indication of laparoscopic partial or total adrenalectomy in patients with aldosterone producing adenoma (APA) remains controversial. We performed the 2 procedures and compared the outcomes of these 2 operations retrospectively. MATERIALS AND METHODS: A total of 92 patients with primary hyperaldosteronism were laparoscopically treated at our institution from 1995 to 2004. A total of 29 patients underwent partial adrenalectomy or enucleation, while unilateral total adrenalectomy was performed in 63. A single pathologist examined the number and histopathological characteristics of APAs. Postoperative median followup was 60.3 and 29.3 months, respectively. RESULTS: Laparoscopic adrenalectomies were successfully performed in each group, although the partial type had fewer ports and shorter operative time. All 63 patients with total adrenalectomy showed recovery from hypertension, suppressed plasma renin activity and high plasma aldosterone. Two of 29 patients with partial adrenalectomy or enucleation still experienced hypertension with high plasma aldosterone. Of the 63 extirpated specimens 17 adrenals (27.0%) demonstrated multiple space occupying lesions along with the main APA. CONCLUSIONS: Primary hyperaldosteronism is highly associated with multiple adrenal space occupying lesions. The risk-to-benefit ratio must be carefully weighed against the potential advantage of partial adrenalectomy. We chose total laparoscopic adrenalectomy in patients with unilateral APA and primary hyperaldosteronism.

All-electron density functional calculation on insulin with quasi-canonical localized orbitals.

An all-electron density functional (DF) calculation on insulin was performed by the Gaussian-based DF program, ProteinDF. Quasi-canonical localized orbitals (QCLOs) were used to improve the initial guess for the self-consistent field (SCF) calculation. All calculations were carried out by parallel computing on eight processors of an Itanium2 cluster (SGI Altix3700) with a theoretical peak performance of 41.6 GFlops. It took 35 h for the whole calculation. Insulin is a protein hormone consisting of two peptide chains linked by three disulfide bonds. The numbers of residues, atoms, electrons, orbitals, and auxiliary functions are 51, 790, 3078, 4439, and 8060, respectively. An all-electron DF calculation on insulin was successfully carried out, starting from connected QCLOs. Regardless of a large molecule with complicated topology, the differences in the total energy and the Mulliken atomic charge between initial and converged wavefunctions were very small. The calculation proceeded smoothly without any trial and error, suggesting that this is a promising method to obtain SCF convergence on large molecules such as proteins.

Reversible restrictive cardiomyopathy due to light-chain deposition disease.

Systemic light-chain deposition due to plasma cell dyscrasias manifests as a form of restrictive cardiomyopathy with diastolic ventricular dysfunction. Although these manifestations are likely to be cardiac amyloidosis, whether these pathological conditions are reversible after treatment of the underlying plasma cell disorders is unknown. To our knowledge, we describe the first patient with cardiac light-chain deposition due to multiple myeloma in whom echocardiographic and biochemical factors of cardiac function were ameliorated dramatically after remission of this disorder. We emphasize that restrictive cardiomyopathy due to light-chain deposition may be reversible and have a relatively better prognosis after remission of plasma cell dyscrasias.