Computational redesign of functional enzymes

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Computational enzyme design for industrially relevant reactions

Cognition of life from the perspective of synthetic biology centers on the design, construction, and characterization of novel biological systems using engineering design principles. Most catalytic functions in living organisms are achieved by enzymes, which serve as key components in synthetic biology. While the amino acid sequence makes up the primary structure of the protein, the chemical/biological properties of the protein are dependent on the three-dimensional or tertiary structure. In the nascent field of synthetic biology, researchers are striving to engineer novel biological functionality based on the structures. The development of computational enzyme design algorithms can provide large amounts of prototype molecules for the synthetic biological devices, especially for new catalytic devices, and also provide templates and guidelines for important components of synthetic biology. As the performance of computational algorithms and design strategies continue to improve, protein designers can construct enzymes from scratch and even create highly proficient biocatalysts. This talk provides a brief overview of design principles of proteins and highlights the latest examples of using computational methods to create enzymes for industrially viable applications. References: R. Li et al. Computational redesign of enzymes for regio-and enantioselective hydroamination, Nature chemical biology, 14 (7), 664 (2018). Y. Bu et al. Engineering improved thermostability of the GH11 xylanase from Neocallimastix patriciarum via computational library design, Applied microbiology and biotechnology, 102 (8), 3675-3685 (2018). B. Wu et al. Versatile peptide C-terminal functionalization via a computationally engineered peptide amidase. ACS Catalysis 6 (8), 5405-5414 (2016)

Black hole masses in narrow-line Seyfert 1 galaxies

The masses of central supermassive black holes in a soft X-ray selected sample of the narrow-line Seyfert 1 galaxies (NLS1s) are estimated by some different methods to test their theoretical models. Apart from the methods using the H$\beta$ linewidth and the [O III] linewidth, soft X-ray excess as a prominent character of NLS1s is used to estimate the black hole masses. The virial mass derived from the H$\beta$ linewidth assuming random orbits of broad-line reigns (BLRs) is consistent with that from the soft X-ray bump luminosity for NLS1s but with a larger scatter. The virial black hole masses showed that most of NLS1s are in the super-Eddington accretion state while most of broad-line Seyfert 1 galaxies (BLS1s) are not. We found that the black hole mass estimated from [O III] linewidth is not in agreement with above two methods. Using the Eddington limit relation for the super-Eddington accretion suggested by Wang (2004), we found that there are 16 NLS1s satisfied with this Eddington limit relation. The masses of these 16 NLS1s derived from X-ray luminosity are systematically larger than that from H$\beta$ linewidth assuming random BLRs orbits. If the mass derived from X-ray luminosity is true, the mean disk inclination to the line of sight in these 16 NLS1s is about $17^{\circ}$, which provided new support for the pole-on orientation effect in NLS1s.Comment: 6 pages, 3 figures, accepted by MNRA

Future prospects of mass-degenerate Higgs bosons in the CPCP-conserving two-Higgs-doublet model

The scenario of two mass-degenerate Higgs bosons within the general two-Higgs-doublet model (2HDM) is revisited. We focus on the global picture when two $CP$-even Higgs bosons of $h$ and $H$ are nearly mass-degenerate. A global fit to the signal strength of the 125 GeV Higgs measured at the LHC is performed. Based on the best-fit result of the 2HDM mixing angles $(\alpha,\beta)$, theoretical constraints, charged and $CP$-odd Higgs boson direct search constraints and the electroweak precision constraints are imposed to the 2HDM parameter space. We present the signal predictions of the $(4b\,, 2b\,2\gamma)$ channels for the benchmark models at the LHC 14 TeV runs. We also study the direct Higgs boson pair productions at the LHC, and the Z-associated Higgs boson pair production search at the ILC 500 GeV runs, as well as the indirect probes at the CEPC 250 GeV run. We find that the mass-degenerate Higgs boson scenario in the Type-II 2HDM can be fully probed by these future experimental searches.Comment: 31 pages, 9 figures, 5 tables, matches with the PRD published versio

Envelope Expansion with Core Collapse. III. Similarity Isothermal Shocks in a Magnetofluid

We explore MHD solutions for envelope expansions with core collapse (EECC) with isothermal MHD shocks in a quasi-spherical symmetry and outline potential astrophysical applications of such magnetized shock flows. MHD shock solutions are classified into three classes according to the downstream characteristics near the core. Class I solutions are those characterized by free-fall collapses towards the core downstream of an MHD shock, while Class II solutions are those characterized by Larson-Penston (LP) type near the core downstream of an MHD shock. Class III solutions are novel, sharing both features of Class I and II solutions with the presence of a sufficiently strong magnetic field as a prerequisite. Various MHD processes may occur within the regime of these isothermal MHD shock similarity solutions, such as sub-magnetosonic oscillations, free-fall core collapses, radial contractions and expansions. We can also construct families of twin MHD shock solutions as well as an `isothermal MHD shock' separating two magnetofluid regions of two different yet constant temperatures. The versatile behaviours of such MHD shock solutions may be utilized to model a wide range of astrophysical problems, including star formation in magnetized molecular clouds, MHD link between the asymptotic giant branch phase to the proto-planetary nebula phase with a hot central magnetized white dwarf, relativistic MHD pulsar winds in supernova remnants, radio afterglows of soft gamma-ray repeaters and so forth.Comment: 21 pages, 33 figures, accepted by MNRA