Murein and pseudomurein cell wall binding domains of bacteria and archaea—a comparative view

The cell wall, a major barrier protecting cells from their environment, is an essential compartment of both bacteria and archaea. It protects the organism from internal turgor pressure and gives a defined shape to the cell. The cell wall serves also as an anchoring surface for various proteins and acts as an adhesion platform for bacteriophages. The walls of bacteria and archaea are mostly composed of murein and pseudomurein, respectively. Cell wall binding domains play a crucial role in the non-covalent attachment of proteins to cell walls. Here, we give an overview of the similarities and differences in the biochemical and functional properties of the two major murein and pseudomurein cell wall binding domains, i.e., the Lysin Motif (LysM) domain (Pfam PF01476) and the pseudomurein binding (PMB) domain (Pfam PF09373) of bacteria and archaea, respectively

Modelowanie numeryczne powierzchni międzyfazowej metal/ciekły żużel w krystalizatorze do ciągłego odlewania stali

The behaviour of liquid slag in the mould is one of the key research areas of the continuous steel casting process. Numerical simulations of steel casting in the mould equipped with submerged entry nozzle, intended for slab casting, have been carried out within the study. For modelling the behaviour of the interfaces of the liquid steel - liquid slag - air system, the VOF method was employed. In the conducted simulations, seven different procedures for the discretization of the interface of individual phases were tested. The computation results have revealed that the “entrapment” of fine slag portions into liquid steel occurs in the system under investigation; the cause of this phenomenon is explicated by the Kelvin-Helmholtz theory.Badania zachowania się ciekłego żużla w krystalizatorze mają istotne znaczenie dla procesu ciągłego odlewania stali. W pracy przeprowadzono symulacje numeryczne odlewania stali w krystalizatorze z wylewem zanurzeniowym, przeznaczonym do odlewania wlewków płaskich. Do modelowania zachowania się granic międzyfazowych układu: ciekła stal – ciekły żużel – powietrze zastosowano metodę Volume of Fluid (VOF). Podczas prowadzonych symulacji weryfikowano siedem różnych procedur dla dyskretyzacji granicy rozdziału poszczególnych faz. Wyniki obliczeń wykazały, że w badanym układzie dochodzi do „zaciągania” drobnych porcji żużla do ciekłej stali, przyczynę tego zjawiska tłumaczy teoria Kelvina-Helmholtza

Modelowanie numeryczne powierzchni międzyfazowej metal/ciekły żużel w krystalizatorze do ciągłego odlewania stali

The behaviour of liquid slag in the mould is one of the key research areas of the continuous steel casting process. Numerical simulations of steel casting in the mould equipped with submerged entry nozzle, intended for slab casting, have been carried out within the study. For modelling the behaviour of the interfaces of the liquid steel - liquid slag - air system, the VOF method was employed. In the conducted simulations, seven different procedures for the discretization of the interface of individual phases were tested. The computation results have revealed that the “entrapment” of fine slag portions into liquid steel occurs in the system under investigation; the cause of this phenomenon is explicated by the Kelvin-Helmholtz theory.Badania zachowania się ciekłego żużla w krystalizatorze mają istotne znaczenie dla procesu ciągłego odlewania stali. W pracy przeprowadzono symulacje numeryczne odlewania stali w krystalizatorze z wylewem zanurzeniowym, przeznaczonym do odlewania wlewków płaskich. Do modelowania zachowania się granic międzyfazowych układu: ciekła stal – ciekły żużel – powietrze zastosowano metodę Volume of Fluid (VOF). Podczas prowadzonych symulacji weryfikowano siedem różnych procedur dla dyskretyzacji granicy rozdziału poszczególnych faz. Wyniki obliczeń wykazały, że w badanym układzie dochodzi do „zaciągania” drobnych porcji żużla do ciekłej stali, przyczynę tego zjawiska tłumaczy teoria Kelvina-Helmholtza

Multiphase Numerical Model of Molten Steel and Slag Behavior in the Continuous Casting Mould

The paper reports the results of numerical simulation of the flow of liquid steel with the use of a multiphase model. The facility under study was a mould designed for continuous casting of steel slabs. The geometry of the facility, along with the computational grid, was generated within the program Ansys-MeshingR. Numerical computations were performed in the programs: COMSOL Multiphysics¯ and Ansys-Fluent¯. The use of the multiphase model enabled the determination of the behavior of the liquid slag layer on the metal bath surface. From the performed computer simulations, the fields of liquid steel motion and liquid steel turbulence kinetic energy distribution in the mould's symmetry plane have been presented. Based on the values recorded at selected measurement points located on the slag surface, a diagram illustrating the variation of the slag layer position during continuous steel casting has been plotted

Physical and Numerical Investigations of Mould Flux Entrainment into Liquid Steel

This paper presents results of model tests, performed in order to analyze phenomenon of slag droplets entrainment into steel in mould, during continuous casting process. The carried out studies took the form of laboratory experiments using physical model, in which – using similarity criteria – the behaviour of interfacial boundary liquid steel-liquid slag has been simulated using water and silicon oils, differing in physicochemical properties. Additionally, based on PIV (Particle Image Velocimetry) measurements and numerical simulations, vector flow field and values of critical velocities, at which observed the occurrence of interfacial boundary silicon oil-water instability have been identified. Based on the carried out investigations, results, that illustrate relationship between critical entrainment velocity and physicochemical properties of oils have been presented

Physical and Numerical Investigations of Mould Flux Entrainment into Liquid Steel

This paper presents results of model tests, performed in order to analyze phenomenon of slag droplets entrainment into steel in mould, during continuous casting process. The carried out studies took the form of laboratory experiments using physical model, in which – using similarity criteria – the behaviour of interfacial boundary liquid steel-liquid slag has been simulated using water and silicon oils, differing in physicochemical properties. Additionally, based on PIV (Particle Image Velocimetry) measurements and numerical simulations, vector flow field and values of critical velocities, at which observed the occurrence of interfacial boundary silicon oil-water instability have been identified. Based on the carried out investigations, results, that illustrate relationship between critical entrainment velocity and physicochemical properties of oils have been presented

Wielofazowy model numeryczny zachowania się ciekłej stali i żużla w krystalizatorze COS

The paper reports the results of numerical simulation of the flow of liquid steel with the use of a multiphase model. The facility under study was a mould designed for continuous casting of steel slabs. The geometry of the facility, along with the computational grid, was generated within the program Ansys-Meshing® . Numerical computations were performed in the programs: COMSOL Multiphysics® and Ansys-Fluent®. The use of the multiphase model enabled the determination of the behavior of the liquid slag layer on the metal bath surface. From the performed computer simulations, the fields of liquid steel motion and liquid steel turbulence kinetic energy distribution in the mould's symmetry plane have been presented. Based on the values recorded at selected measurement points located on the slag surface, a diagram illustrating the variation of the slag layer position during continuous steel casting has been plotted.W niniejszej pracy przedstawiono wyniki symulacji numerycznej przepływu ciekłej stali z wykorzystaniem modelu wielofazowego. Badanym obiektem był krystalizator przeznaczony do ciągłego odlewania stalowych wlewków płaskich. Geometrię obiektu wraz z siatkę obliczeniową wygenerowano w programie Ansys-Meshing®. Obliczenia numeryczne wykonano w programach: COMSOL Multiphysics® i Ansys-Fluent®. Zastosowanie modelu wielofazowego pozwoliło na określenie zachowania się warstwy ciekłego żużla na powierzchni kąpieli metalowej. Na podstawie wykonanych symulacji komputerowych zaprezentowano pola ruchu ciekłej stali oraz rozkładu kinetycznej energii turbulencji ciekłej stali w płaszczyźnie symetrii krystalizatora. Bazując na wartościach zarejestrowanych w wybranych punktach pomiarowych, znajdujących się na powierzchni żużla, sporządzono wykres obrazujący zmianę położenia warstwy żużla podczas ciągłego odlewania stali

Numerical Modelling of Metal/Flux Interface in a Continuous Casting Mould / Modelowanie Numeryczne Powierzchni Międzyfazowej Metal/Ciekły Żużel W Krystalizatorze Do Ciągłego Odlewania Stali

The behaviour of liquid slag in the mould is one of the key research areas of the continuous steel casting process. Numerical simulations of steel casting in the mould equipped with submerged entry nozzle, intended for slab casting, have been carried out within the study. For modelling the behaviour of the interfaces of the liquid steel - liquid slag - air system, the VOF method was employed. In the conducted simulations, seven different procedures for the discretization of the interface of individual phases were tested. The computation results have revealed that the “entrapment” of fine slag portions into liquid steel occurs in the system under investigation; the cause of this phenomenon is explicated by the Kelvin-Helmholtz theory

Insights into the Molecular Activation Mechanism of the RhoA-specific Guanine Nucleotide Exchange Factor, PDZRhoGEF

PDZRhoGEF (PRG) belongs to a small family of RhoA-specific nucleotide exchange factors that mediates signaling through select G-protein-coupled receptors via Gα(12/13) and activates RhoA by catalyzing the exchange of GDP to GTP. PRG is a multidomain protein composed of PDZ, regulators of G-protein signaling-like (RGSL), Dbl-homology (DH), and pleckstrin-homology (PH) domains. It is autoinhibited in cytosol and is believed to undergo a conformational rearrangement and translocation to the membrane for full activation, although the molecular details of the regulation mechanism are not clear. It has been shown recently that the main autoregulatory elements of PDZRhoGEF, the autoinhibitory "activation box" and the "GEF switch," which is required for full activation, are located directly upstream of the catalytic DH domain and its RhoA binding surface, emphasizing the functional role of the RGSL-DH linker. Here, using a combination of biophysical and biochemical methods, we show that the mechanism of PRG regulation is yet more complex and may involve an additional autoinhibitory element in the form of a molten globule region within the linker between RGSL and DH domains. We propose a novel, two-tier model of autoinhibition where the activation box and the molten globule region act synergistically to impair the ability of RhoA to bind to the catalytic DH-PH tandem. The molten globule region and the activation box become less ordered in the PRG-RhoA complex and dissociate from the RhoA-binding site, which may constitute a critical step leading to PRG activation

The solution structure and dynamics of the DH-PH module of PDZRhoGEF in isolation and in complex with nucleotide-free RhoA

The DH-PH domain tandems of Dbl-homology guanine nucleotide exchange factors catalyze the exchange of GTP for GDP in Rho-family GTPases, and thus initiate a wide variety of cellular signaling cascades. Although several crystal structures of complexes of DH-PH tandems with cognate, nucleotide free Rho GTPases are known, they provide limited information about the dynamics of the complex and it is not clear how accurately they represent the structures in solution. We used a complementary combination of nuclear magnetic resonance (NMR), small-angle X-ray scattering (SAXS), and hydrogen-deuterium exchange mass spectrometry (DXMS) to study the solution structure and dynamics of the DH-PH tandem of RhoA-specific exchange factor PDZRhoGEF, both in isolation and in complex with nucleotide free RhoA. We show that in solution the DH-PH tandem behaves as a rigid entity and that the mutual disposition of the DH and PH domains remains identical within experimental error to that seen in the crystal structure of the complex, thus validating the latter as an accurate model of the complex in vivo. We also show that the nucleotide-free RhoA exhibits elevated dynamics when in complex with DH-PH, a phenomenon not observed in the crystal structure, presumably due to the restraining effects of crystal contacts. The complex is readily and rapidly dissociated in the presence of both GDP and GTP nucleotides, with no evidence of intermediate ternary complexes