FoldX as Protein Engineering Tool: Better Than Random Based Approaches?

Improving protein stability is an important goal for basic research as well as for clinical and industrial applications but no commonly accepted and widely used strategy for efficient engineering is known. Beside random approaches like error prone PCR or physical techniques to stabilize proteins, e.g. by immobilization, in silico approaches are gaining more attention to apply target-oriented mutagenesis. In this review different algorithms for the prediction of beneficial mutation sites to enhance protein stability are summarized and the advantages and disadvantages of FoldX are highlighted. The question whether the prediction of mutation sites by the algorithm FoldX is more accurate than random based approaches is addressed

Enantiomer discrimination in β-phenylalanine degradation by a newly isolated Paraburkholderia strain BS115 and type strain PsJN

Despite their key role in numerous natural compounds, β-amino acids have rarely been studied as substrates for microbial degradation. Fermentation of the newly isolated Paraburkholderia strain BS115 and the type strain P. phytofirmans PsJN with β-phenylalanine (β-PA) as sole nitrogen source revealed (S)-selective transamination of β-PA to the corresponding β-keto acid by both strains, accompanied by substantial formation of acetophenone (AP) from spontaneous decarboxylation of the emerging β-keto acid. While the PsJN culture became stationary after entire (S)-β-PA consumption, BS115 showed further growth at a considerably slower rate, consuming (R)-β-PA without generation of AP which points to a different degradation mechanism for this enantiomer. This is the first report on degradation of both enantiomers of any β-amino acid by one single bacterial strain

FoldX as Protein Engineering Tool: Better Than Random Based Approaches?

Improving protein stability is an important goal for basic research as well as for clinical and industrial applications but no commonly accepted and widely used strategy for efficient engineering is known. Beside random approaches like error prone PCR or physical techniques to stabilize proteins, e.g. by immobilization, in silico approaches are gaining more attention to apply target-oriented mutagenesis. In this review different algorithms for the prediction of beneficial mutation sites to enhance protein stability are summarized and the advantages and disadvantages of FoldX are highlighted. The question whether the prediction of mutation sites by the algorithm FoldX is more accurate than random based approaches is addressed. Keywords: FoldX, Fold-X, Thermostability, Protein stabilization, Protein engineering, Enzyme engineerin

Enantiomer discrimination in β-phenylalanine degradation by a newly isolated Paraburkholderia strain BS115 and type strain PsJN

Abstract Despite their key role in numerous natural compounds, β-amino acids have rarely been studied as substrates for microbial degradation. Fermentation of the newly isolated Paraburkholderia strain BS115 and the type strain P. phytofirmans PsJN with β-phenylalanine (β-PA) as sole nitrogen source revealed (S)-selective transamination of β-PA to the corresponding β-keto acid by both strains, accompanied by substantial formation of acetophenone (AP) from spontaneous decarboxylation of the emerging β-keto acid. While the PsJN culture became stationary after entire (S)-β-PA consumption, BS115 showed further growth at a considerably slower rate, consuming (R)-β-PA without generation of AP which points to a different degradation mechanism for this enantiomer. This is the first report on degradation of both enantiomers of any β-amino acid by one single bacterial strain

β-Phenylalanine Ester Synthesis from Stable β-Keto Ester Substrate Using Engineered ω-Transaminases

The successful synthesis of chiral amines from ketones using ω-transaminases has been shown in many cases in the last two decades. In contrast, the amination of β-keto acids is a special and relatively new challenge, as they decompose easily in aqueous solution. To avoid this, transamination of the more stable β-keto esters would be an interesting alternative. For this reason, ω-transaminases were tested in this study, which enabled the transamination of the β-keto ester substrate ethyl benzoylacetate. Therefore, a ω-transaminase library was screened using a coloring o-xylylenediamine assay. The ω-transaminase mutants 3FCR_4M and ATA117 11Rd show great potential for further engineering experiments aiming at the synthesis of chiral (S)- and (R)-β-phenylalanine esters. This alternative approach resulted in the conversion of 32% and 13% for the (S)- and (R)-enantiomer, respectively. Furthermore, the (S)-β-phenylalanine ethyl ester was isolated by performing a semi-preparative synthesi

Dynamic Behavior of Tin at Platinum Surfaces during Catalytic CO Oxidation

Platinum–tin surfaces are active for CO oxidation, but their activity and the effects of tin oxide phases that form under reaction conditions are poorly understood. We have studied surface alloys of tin prepared on platinum single crystals during catalytic CO oxidation using near-ambient-pressure X-ray photoemission spectroscopy. On the flat terraces of Sn/Pt(111), a wetting layer of Sn(II) surface oxide forms, while on the stepped Sn/Pt(223) surface, 3D clusters of Sn(IV) oxide are formed. Oxidation of tin by O2 competes with the reduction of the oxides by CO under reaction conditions. Oxides that do not completely cover the surface can be reduced to metallic tin, while a fully covering layer of Sn(II) oxide cannot, showing the importance of oxide edge sites for the reduction process. The samples where 2D oxide layers are formed show a higher CO oxidation activity than for pure platinum at low temperatures, while the Sn(IV) oxide clusters on the stepped surfaces do not affect the measured CO oxidation rate. We therefore identify 2D Sn(II) oxide as an active phase for CO oxidation. While oxide island edges appear to make only minor contributions to conversion under these conditions, reactions at these sites play a major role in determining the phases present and their transformations

Oxygen Storage by Tin Oxide Monolayers on Pt3Sn(111)

The high performance of platinum–tin catalysts for oxidation reactions has been linked to the formation of tin oxides at the metal surface, but little is known about the structure of these oxides or the chemical behavior that determines their catalytic properties. We show here how surface oxides on Pt3Sn(111) incorporate oxygen at the metal interface, which may be subsequently removed by reaction with CO. The storage mechanism, where oxygen uptake occurs without loss of interfacial Pt–Sn bonds, is enabled by the peculiar asymmetrical coordination state of Sn2+. O atoms are bound at pocket sites in the 2D oxide sheet between these outward-buckled Sn atoms and metallic Sn in the alloy surface below.

Dynamic Behavior of Tin at Platinum Surfaces during Catalytic CO Oxidation

Platinum–tin surfaces are active for CO oxidation, but their activity and the effects of tin oxide phases that form under reaction conditions are poorly understood. We have studied surface alloys of tin prepared on platinum single crystals during catalytic CO oxidation using near-ambient-pressure X-ray photoemission spectroscopy. On the flat terraces of Sn/Pt(111), a wetting layer of Sn(II) surface oxide forms, while on the stepped Sn/Pt(223) surface, 3D clusters of Sn(IV) oxide are formed. Oxidation of tin by O2 competes with the reduction of the oxides by CO under reaction conditions. Oxides that do not completely cover the surface can be reduced to metallic tin, while a fully covering layer of Sn(II) oxide cannot, showing the importance of oxide edge sites for the reduction process. The samples where 2D oxide layers are formed show a higher CO oxidation activity than for pure platinum at low temperatures, while the Sn(IV) oxide clusters on the stepped surfaces do not affect the measured CO oxidation rate. We therefore identify 2D Sn(II) oxide as an active phase for CO oxidation. While oxide island edges appear to make only minor contributions to conversion under these conditions, reactions at these sites play a major role in determining the phases present and their transformations

Wafer-Scale Synthesis of Graphene on Sapphire: Toward Fab-Compatible Graphene

The adoption of graphene in electronics, optoelectronics and photonics is hindered by the difficulty in obtaining high quality material on technologically-relevant substrates, over wafer-scale sizes and with metal contamination levels compatible with industrial requirements. To date, the direct growth of graphene on insulating substrates has proved to be challenging, usually requiring metal-catalysts or yielding defective graphene. In this work, we demonstrate a metal-free approach implemented in commercially available reactors to obtain high-quality monolayer graphene on c-plane sapphire substrates via chemical vapour deposition (CVD). We identify via low energy electron diffraction (LEED), low energy electron microscopy (LEEM) and scanning tunneling microscopy (STM) measurements the Al-rich reconstruction root31R9 of sapphire to be crucial for obtaining epitaxial graphene. Raman spectroscopy and electrical transport measurements reveal high-quality graphene with mobilities consistently above 2000 cm2/Vs. We scale up the process to 4-inch and 6-inch wafer sizes and demonstrate that metal contamination levels are within the limits for back-end-of-line (BEOL) integration. The growth process introduced here establishes a method for the synthesis of wafer-scale graphene films on a technologically viable basis.Comment: 15 main text pages, 4 main text figures, 13 supplementary information pages, 12 supplementary figures, 3 supplementary table