Large-scale Domain Research Articles

Abstract 1597: Real-world large-scale study kinase domain duplications across diverse tumor types in Chinese populations

Abstract Background: Recently, kinase domain duplications (KDD) in BRAF, EGFR, MET and FGFR1 were reported, along with responses to tyrosine kinase inhibitors (TKI). However, its frequency and clinical outcomes in advanced cancer patients are larglely uncertain. We assessed the frequency of KDD across 14, 491 advanced cancers to reveal the landscape in a wide variety of subtypes. Methods: A multicenter study in China was initiated from July 2013, and advanced cancer patients have been enrolled as of September 2018. We analyzed data from 14, 491 clinical advanced cancer cases, each of which had results from next-generation sequencing (NGS)-based 381 genes panel assay, analogous to the index patient. Results: Of this entire cohort [6837 lung cancer (47.18%), 1894 breast cancer (13.07%), 1325 colorectal cancer (9.14%), 710 urinary system tumor (4.90%), 536 gynecological tumor (3.70%), 592 hepatobiliary cancer (4.09%), 221 gastric cancer (1.53%), 312 soft tissue sarcoma (2.15%), 260 head and neck cancer (1.79%) and 1804 others (12.45%)], 71 patients were identified with KDD, including EGFR (16), BRAF (12), MET (11), FGFR3 (8), RET (3), PDGFRA (3), ROS1 (3), FGFR1 (2), ERBB2 (2), SOX17 (2), ALK (2), KIT (1), NTRK1 (1), BAP1 (1), TMPRSS2 (1), ERBB4 (1), VHL (1), NTRK3 (1). KDD were seen in 0.39% (27/6837) of lung cancer [EGFR(9), BRAF (2), MET (6), FGFR3 (2), RET (1), PDGFRA (1), ROS1 (2), ERBB2 (1), ALK (1), NTRK1 (1), and ERBB4 (1)]; 0.21%(4/1894) of breast cancer [BRAF (1), FGFR3 (2), FGFR1 (1)]; 0.60%(8/1325) of colorectal cancer [EGFR (1), BRAF (3), FGFR3 (2), RET (1), ROS1 (1)]; 0.28%(2/710) of urinary system tumor [TMPRSS2(1), VHL (1)]; 0.19%(1/536) of gynecological tumor [SOX17 (1)]; 0.17%(1/592) of hepatobiliary cancer [EGFR (1)]; 0.45%(1/221) of gastric cancer [ERBB2 (1)]; 0.96%(3/312) of soft tissue sarcoma [EGFR (1), FGFR3 (1), PDGFRA (1)]; 0.77%(2/260) of head and neck cancer [BRAF (2)]; and 1.22%(22/1804) of others [EGFR (4), BRAF (4), MET (5), FGFR3 (1), RET (1), PDGFRA (1), FGFR1 (1), SOX17 (1), ALK (1), KIT (1), BAP1 (1), and NTRK3 (1)]; KDD possibly related to target resistance were seen in ERBB2 amplification gastric cancer and ALK-related NSCLC. Conclusion: Diverse KDD are found across diverse tumor types and may underlie acquired resistance, and can benefit from matched targeted treatment. In addition, for short- or long-term responses to targeted treatment, we can use the NGS assay to explore differential gene alter in the future. Citation Format: Chun-wei Xu, Wen-xian Wang, Xiao-jia Wang, You-cai Zhu, Qu-xia Zhang, Yong Fang, Xiu-yu Cai, Yu Chen, Li Lin, Hong Wang, Mei-yu Fang, Yin-bin Zhang, Shi-jie Lan, Xin Liu, Xing-xiang Pu, Zong-yang Yu, Bing Wan, Jian-ying Li, Xian-bin Liang, Li-ping Wang, Wu Zhuang, Ling Lin, Gang Chen, Tang-feng Lv, Yong Song. Real-world large-scale study kinase domain duplications across diverse tumor types in Chinese populations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1597.

Investigation of the microstructure adjustment by velocity variations during the directional solidification of Al-Ag-Cu with the phase-field method

Directional solidification is a favored process to manufacture homogeneous microstructures which lead to macroscopically unique properties for a material. The dependence of the spacing and type of the arising microstructure from the solidification velocity for constant velocities is extensively investigated. However the effect of changes in the solidification velocity on the resulting microstructure adjustment processes is still unclear. Therefore large-scale (3D+t) simulations of the ternary eutectic system Ag-Al-Cu with changing solidification velocities are conducted with a phase-field model based on the grand potential approach. To study the spatially complex rearrangement process during velocity changes in statistical representative volume elements, simulations with different velocity profiles are calculated in large-scale domains. The results show, that the evolving microstructure continuously rearranges by splitting and merging of the rods despite constant growth conditions. By increasing the velocity, the microstructure refines by splitting of the Al2Cu phase. Whereas by decreasing the velocity, the microstructure coarsens by overgrowing events of both intermetallic phases.

Role of the Hydrophilic Latex Particle Surface in Water Diffusion into Films from Waterborne Polymer Colloids.

The diffusion mechanism and growth of large-scale domains during the immersion of latex films in water have been thoroughly investigated with scattering techniques in a combination with the gravimetric method. Latex dispersions for film formation studies had identical main monomer compositions and only differ in the hydrophilic comonomers that result in distinct "hairy" layer structures of the particles. The major effects of the presence and the structure of the surface layers were identified: (1) Introducing the hydrophilic surface layer in the binder structure results in a more uniform penetration of water and a reduction in the water domain growth. (2) The nature of the particle shell defines the rate of the formation of the first hydration layer and the beginning of the large cluster formation. Poly(acrylamide) in the particle shell promotes the formation of the homogeneously swollen film and slows down the development of water "pockets." Poly(acrylic acid) leads to a more heterogeneous material and accelerates water uptake and cluster growth. (3) The thickness of the particle hairy layer regulates the thickness of the interstitials in the dry film and the number of the chemical groups involved in H-bonding with water molecules without a cluster formation. The amount of water that was absorbed before large domains start evolving increased with the growth of the particle shell thickness.

Multiscale structural optimization towards three-dimensional printable structures

This paper develops a robust framework for the multiscale design of three-dimensional lattices with macroscopically tailored structural characteristics. The work exploits the high process flexibility and precision of additive manufacturing to the physical realization of complex microstructure of metamaterials by developing and implementing a multiscale approach. Structures derived from such metamaterials exhibit properties which differ from that of the constituent base material. A periodic microscale model is developed whose geometric parameterization enables smoothly changing properties and for which the connectivity of neighboring microstructures in the large-scale domain is guaranteed by slowly changing large-scale descriptions of the lattice parameters. A lattice-based functional grading of material is derived using the finite element method with sensitivities derived by the adjoint method. The novelty of the work lies in the use of multiple geometry-based small-scale design parameters for optimization problems in three-dimensional real space. The approach is demonstrated by solving a classical compliance minimization problem. The results show improved optimality compared to commonly implemented structural optimization algorithms.

Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase.

Enzymes in the prolyl oligopeptidase family possess unique structures and substrate specificities that are important for their biological activity and for potential biocatalytic applications. The crystal structures of Pyrococcus furiosus ( Pfu) prolyl oligopeptidase (POP) and the corresponding S477C mutant were determined to 1.9 and 2.2 Å resolution, respectively. The wild type enzyme crystallized in an open conformation, indicating that this state is readily accessible, and it contained bound chloride ions and a prolylproline ligand. These structures were used as starting points for molecular dynamics simulations of Pfu POP conformational dynamics. The simulations showed that large-scale domain opening and closing occurred spontaneously, providing facile substrate access to the active site. Movement of the loop containing the catalytically essential histidine into a conformation similar to those found in structures with fully formed catalytic triads also occurred. This movement was modulated by chloride binding, providing a rationale for experimentally observed activation of POP peptidase catalysis by chloride. Thus, the structures and simulations reported in this study, combined with existing biochemical data, provide a number of insights into POP catalysis.

A Multi-State Coarse-Grained Simulation Model Captures Conformational Cycling in P-Type ATPases

P-type ATPases are a large family of ion pumps that precisely move ions into and out of cell membrane against their concentration gradients by consuming ATP. All the family members share a common basic pump cycle (also known as the Post-Albers cycle) consisting of two main conformational states (termed E1 and E2) with distinct conformations and affinities for the primary transported ions. Over 120 high-resolution structures of P-type ATPases have been accumulated in the Protein Data Bank (PDB), with most of the available structures being of the sarcoplasmic reticulum Ca2+-ATPase (SERCA, ∼60%) and the Na+/K+-ATPase (NKA, ∼30%). While these experimentally-derived structures capture the ATPases in a variety of conformational states, and thus provide crucial insight into transport mechanism, they do not directly reveal how the conformational changes occur, and how signals are transferred between the transmembrane regions and the cytoplasmic domains consisting of the phosphorylation (P) domain, the nucleotide binding (N) domain and the actuator (A) domain. To bridge the missing dynamics information between static structures during the Post-Albers cycle, we have developed a coarse-grained model by combining a multi-basin structure-based potential with a modified implicit solvent MARTINI model and enhance sampling using metadynamics simulations. The model allows access the millisecond dynamics and large-scale domain motions of such large membrane proteins with more than a thousand of residues. In this way we are able to capture conformational changes between the E1-E2 states of SERCA and NKA and obtain more detailed information about the mechanisms underlying transport function and regulation.

Distribution and existing forms of trace elements from Maliping Pb-Zn deposit in northeastern Yunnan, China: A LA-ICPMS study

The Sichuan-Yunnan-Guizhou (SYG) Pb-Zn metallogenic province, located in southwestern margin of the Yangtze Block, is an important part of the large-scale low-temperature metallogenic domain in southwestern China. The Maliping Pb-Zn deposit, situated in the central part of Zhaotong-Qujing metallogenic belt, was found in northeastern Yunnan Province recently. The orebody is hosted in Late Cambrian Yuhucun Formation, occurring as stratabound, lense and venis. The mineral assemblage of the Maliping deposit is relatively simple. The main sulfide minerals are sphalerite and galena with minor pyrite. Gangue minerals include mainly dolomite, calcite, quartz and barite. LA-ICPMS spots and mapping analysis for the different sulfides from Maliping Pb-Zn deposit, and the distribution and existing forms of germanium, cadmium, indium and other trace elements were investigated. The results show that different sulfides are characterized by different contents of trace elements. Mn, Cu, Sn, Cd, In and Ge are mainly enriched in sphalerite, while galena from this deposit is enrichment of Ag, Sb and Se, and pyrite is characterized by enrichment of As, Co and Ni. Comparing with the content of dispersed elements in different sulfides, the results indicate that sphalerite is the primary carrier mineral of Ge, In and Cd. Cd, Ge, In, Mn, As, Sb and Ag occur as isomorphous substitution in the sphalerite, and Cu mostly exists in sphalerite as isomorphism but part of Cu occurs as micro-inclusions (chalcopyrite) in sphalerite. Considered the distinct positive relationship between Cu and Ge, the results imply that the substitution mechanism of Ge and Cu is possibly 3Zn2+↔Ge4++2Cu+. Additionally, sphalerite from Maliping Pb-Zn deposit is characterized by enrichment of Cd, Ge and depleted in Mn, Fe, Co and Sn which coincides with the feature of MVT Pb-Zn deposit and differs from the sedimentary-exhalative deposit and magmatic-hydrothermal deposit. On account of the geological features, other geochemical researches and its ore-forming temperature belonging to low temperature, it is suggested that the Maliping deposit belongs to an MVT Pb-Zn deposit. Notably, we imply that ore-forming fluid extracted indium of magmatic and volcaniclastic rocks from the metamorphic basement, resulting in the enrichment of indium in sphalerite from the deposit.

The trace (dispersed) elements in pyrite from the Fule Pb-Zn deposit, Yunnan Province, China, and its genetic information: A LA-ICPMS study

The Sichuan-Yunnan-Guizhou Pb-Zn mineralization province (SYGMP) is an important part of the large-scale low-temperature metallogenic domain in Southwest China. There is always controversy on whether the Pb-Zn deposits in the SYGMP belong to a MVT-type. Additionally, these deposits are mainly characterized by enrichment in dispersed elements (especially Ge) which is chiefly hosted in sphalerite. Owing to the lack of study on trace elements in pyrite, in this paper, we analyzed the characteristics of trace (including dispersed) elements in pyrite from the Fule Pb-Zn deposit by LA-ICPMS, showing that the pyrite is one of carrier minerals of Ge except the sphalerite. Three samples were collected from Fule and Fusheng ore blocks, which represent ore bodies in level 1350, 1410 and 1536 meters, respectively, i.e. from deep to shallow. The results show that the pyrites are characterized by enrichment of Cu, As, Co and Ni, and local high contents of Pb (Sb) and Zn are identified as micro-inclusions like galena and sphalerite. The dispersed elements in pyrite are typically recognized by enrichment of Se and Ge, together with minor Tl and Te. Most of the dispersed elements occur as isomorphous substitution in the pyrite, except Cd and In which principally hosted in Zn-bearing micro-inclusions (sphalerite) as isomorphous substitution too. The strongly positive correlations between Ge and Cu in the pyrite indicate the replacement mechanism is Cu2++Ge2+↔2Fe2+. The enrichment of dispersed elements in pyrite is closely related to the enrichment of ore-forming elements, especially Cu. With the development of the mineralization (ore-bodies from deep to shallow), the Se/Te ratios, dispersed and ore-forming elements are concentrated gradually. Most of the Co/Ni ratios are less than 1.00, suggesting pyrites have experienced a sedimentary-reworked process. In the scattergrams of the Co-Ni and dispersed elements Se-Tl, pyrites from the Fule deposit were plotted within the field of typical MVT deposit, and are different from that of pyrites in the SEDEX, VMS and skarn deposits. Combining the evidence of the geological features, the Fule deposit is similar to MVT deposit, it is suggested the Fule Pb-Zn deposit belong to a MVT-type deposit.

Scalable complex event processing using adaptive load balancing

An essential requirement of large-scale event-driven systems is the real-time detection of complex patterns of events from a large number of basic events and derivation of higher-level events using complex event processing (CEP) mechanisms. Centralized CEP mechanisms are however not scalable and thus inappropriate for large-scale domains with many input events and complex patterns, rendering the horizontal scaling of CEP mechanisms a necessity. In this paper, we propose CCEP as a mechanism for clustering of heterogeneous CEP engines to provide horizontal scalability using adaptive load balancing. We experimentally compare the performance of CCEP with the performances of three CEP clustering mechanisms, namely VISIRI, SCTXPF, and RR. The results of experiments show that CCEP increases throughput by 40 percent and thus it is more scalable than the other three chosen mechanisms when the input event rate changes at runtime. Although CCEP increases the network utilization by about 40 percent, it keeps the load of the system two times more balanced and reduces the input event loss three times.

Effect of large-scale domain switching on intensity factors for a crack in 3D ferroelectric single crystals using the I-integral method

Due to their intrinsic brittleness, ferroelectric materials are prone to fracture under extreme electromechanical operational loads. The fracture of ferroelectric materials is usually accompanied by large-scale domain switching. This paper develops the interaction integral (I-integral) method for a crack in three-dimensional ferroelectrics through applying a virtual load increment to the current state. Unlike the widely-used switching-toughening model, the I-integral is not restricted to small scale switching. Due to designable choice of the virtual load increment, the I-integral allows to decouple the intensity factors of different fracture modes. The local intensity factors along the curved crack front can be directly extracted, since the I-integral is independent of integration volume. With these merits, the I-integral method is a very promising technique in fracture analysis of ferroelectrics under large-scale domain switching. Moreover, the I-integral method is used in combination with the phase field model to simulate a tensile test of nanoscale PbTiO3 ferroelectric single crystal with a semi-circular surface crack. Results show that various patterns of polarization pairs appear as soon as the applied load is increased beyond a critical value. The stable domain structures are divided into two layers by the plane where the crack is located and in each layers several polarization vortices formed eventually. Apart from the geometry and loading conditions, the position where the crack front is located with respect to the polarization vortex is a key factor affecting the switching-induced change of the stress intensity factor.

Interpretation of regional-scale distribution of high Hg in soils of karst area in southwest China

The abundance and spatial distribution of mercury in soil samples covering nearly the whole of China ( c . 9 million km 2 ) were obtained by the China Geochemical Baseline (CGB) project from 2008 to 2015. From the data and maps, it was found that the Hg contents both in the top (0–25 cm) and deep soil (below 100 cm or C-horizon) of the karst area in southwestern China are richer than that of any other geographical landscape areas. Median Hg values for this karst area are 113 and 90 µg/kg respectively ( n = 126), in the top and bottom soils, much higher than the corresponding data of 26 and 18 µg/kg for the entire country ( n = 3380). This regional-scale high Hg distribution is due mainly to high Hg geochemical backgrounds in bedrock and soil formation on limestone. A large-scale epithermal metallogenic domain developed in southwestern China and the extensive distribution of Lower Cambrian black shale in southwest China led to a high Hg geochemical background for parent rocks of soils. The chemical weathering of carbonate minerals and the geochemical behaviour of Hg in the epigenetic environment result in Hg enrichment by ferric oxides, iron hydroxide and organic carbon in limestone soils. Human activities mostly result in local-scale Hg anomalies, but have little effect on this regional-scale anomaly.

COPCOP: A Novel Algorithm and Parallel Optimization Framework for Co-Evolutionary Domain Detection.

Co-evolution exists ubiquitously in biological systems. At the molecular level, interacting proteins, such as ligands and their receptors and components in protein complexes, co-evolve to maintain their structural and functional interactions. Many proteins contain multiple functional domains interacting with different partners, making co-evolution of interacting domains occur more prominently. Multiple methods have been developed to predict interacting proteins or domains within proteins by detecting their co-variation. This strategy neglects the fact that interacting domains can be highly co-conserved due to their functional interactions. Here we report a novel algorithm COPCOP to detect signals of both co-positive selection (co-variation) and co-purifying selection (co-conservation). Results show that our algorithm performs well and outperforms the popular co-variation analysis program CAPS. We also design and implement a multi-level parallel acceleration strategy for COPCOP based on Tianhe-2 CPU-MIC heterogeneous supercomputer system to meet the need of large-scale co-evolutionary domain detection.

Quantifying uncertainty in simulated streamflow and runoff from a continental-scale monthly water balance model

Abstract One important component of continental-scale hydrologic modeling is quantifying the level of uncertainty in long-term hydrologic simulations and providing a range of possible simulated streamflow and/or runoff values for gaged and ungaged locations. In this paper, uncertainty was quantified for simulated streamflow and runoff generated from a monthly water balance model (MWBM) at 1575 streamgages and 109,951 hydrologic response units (HRUs), which span the conterminous United States (CONUS). A stochastic-approach, which incorporated the properties of modeled streamflow residuals back into the simulated model output, was used to create time series of upper and lower uncertainty intervals (UIs) around the simulated monthly time series. This approach was applied to an existing hydrologic regionalization implementation. Metrics used to evaluate the UIs across the CONUS (the coverage ratio, average width index, and interval skill score) indicated that on average the UIs were reliable, skillful, and sharp in being able to both contain measured streamflow observations and reduce estimates of uncertainty based on expected model predictions. These uncertainty evaluation metrics can complement each other in characterizing model skill and uncertainty over large-scale domains.

Thermal kinetic inductance detectors for soft X-ray spectroscopy

Abstract Superconducting microwave microresonators are low temperature detectors (LTDs) suitable for large-scale frequency domain multiplexing readout. A promising approach consists in operating the resonators in quasi-thermal equilibrium mode: the resonator acts as a thermometer sensing the temperature rise of an absorbing material caused by an energy release. Our aim is to develop such detectors to perform spectroscopy in the keV range, with a possible future application to a next generation experiment aimed at directly measuring the neutrino mass . Still, the best configuration in terms of detector design and material must be found. Resonators made of several Ti/TiN multilayer films, which is a high kinetic inductance superconducting material previously developed by our group, were recently produced. The resonators are deposited onto a silicon slab and the sensitive area, thermally coupled to a gold absorber, is kept suspended by means of a SiN x membrane. In this way we plan to exploit the excellent energy resolution of LTDs combined with the simple multiplexing scheme of the resonators. In this contribution we present the devices along with our project, with its status and perspectives.

Study of magnetic reconnection in large-scale magnetic island coalescence via spatially coupled MHD and PIC simulations

We study the process of magnetic reconnection in a coalescing magnetic island setup by means of numerical simulation. This process mimics flux tube merging which can take place in the solar corona, laboratory, and astrophysical objects. Simulations are performed with magnetohydrodynamics (MHD), Hall-MHD, and a newly developed Coupled MHD and Particle-In-Cell (PIC) model (CMAP). This model treats the global simulation domain with MHD, while the region around the reconnection zone is treated with PIC. This CMAP code allows us to simulate larger-scale domains with lesser computing power compared to fully PIC simulations. CMAP reproduces the dynamics of fully kinetic simulations which Hall-MHD does not capture, as seen in the Hall magnetic field and the reconnecting current sheet structure. For large islands in kinetic simulations, the current sheet does not form smoothly and shows chaotic behavior, and the magnetic islands also bounce and slosh. The current sheet thickness, length, and aspect ratios are calculated. They show that in the CMAP model, the thickness remains close to the ion skin depth, while the length changes weakly with the system size, giving a steady aspect ratio for the two largest system size simulations. The pressure tensor also shows large deviations from isotropy and gyrotropy near the current sheet. The CMAP simulations for smaller system sizes are compared to fully kinetic simulations, and we find that a minimum fraction of area has to be provided PIC feedback in the CMAP simulations in order to produce reconnection rates and dynamics similar to fully kinetic simulations. The reconnection rate reduces with the increasing island size. For the CMAP model, this reduction is steeper compared to MHD and Hall-MHD initially, but for larger system sizes, the reconnection rates in CMAP simulations show a steady behavior.

Rich Chromatin Structure Prediction from Hi-C Data.

Recent studies involving the 3-dimensional conformation of chromatin have revealed the important role it has to play in different processes within the cell. These studies have also led to the discovery of densely interacting segments of the chromosome, called topologically associating domains. The accurate identification of these domains from Hi-C interaction data is an interesting and important computational problem for which numerous methods have been proposed. Unfortunately, most existing algorithms designed to identify these domains assume that they are non-overlapping whereas there is substantial evidence to believe a nested structure exists. We present a methodology to predict hierarchical chromatin domains using chromatin conformation capture data. Our method predicts domains at different resolutions, calculated using intrinsic properties of the chromatin data, and effectively clusters these to construct the hierarchy. At each individual level, the domains are non-overlapping in such a way that the intra-domain interaction frequencies are maximized. We show that our predicted structure is highly enriched for actively transcribing housekeeping genes and various chromatin markers, including CTCF, around the domain boundaries. We also show that large-scale domains, at multiple resolutions within our hierarchy, are conserved across cell types and species. We also provide comparisons against existing tools for extracting hierarchical domains. Our software, Matryoshka, is written in C++11 and licensed under GPL v3; it is available at https://github.com/COMBINE-lab/matryoshka.

Mechanism of parkin activation by PINK1.

Mutations in the E3 ubiquitin ligase parkin (PARK2, also known as PRKN) and the protein kinase PINK1 (also known as PARK6) are linked to autosomal-recessive juvenile parkinsonism (AR-JP)1,2; at the cellular level, these mutations cause defects in mitophagy, the process that organizes the destruction of damaged mitochondria3,4. Parkin is autoinhibited, and requires activation by PINK1, which phosphorylates Ser65 in ubiquitin and in the parkin ubiquitin-like (Ubl) domain. Parkin binds phospho-ubiquitin, which enables efficient parkin phosphorylation; however, the enzyme remains autoinhibited with an inaccessible active site5,6. It is unclear how phosphorylation of parkin activates the molecule. Here we follow the activation of full-length human parkin by hydrogen-deuterium exchange mass spectrometry, and reveal large-scale domain rearrangement in the activation process, during which the phospho-Ubl rebinds to the parkin core and releases the catalytic RING2 domain. A 1.8Å crystal structure of phosphorylated human parkin reveals the binding site of the phospho-Ubl on the unique parkin domain (UPD), involving a phosphate-binding pocket lined by AR-JP mutations. Notably, a conserved linker region between Ubl and the UPD acts as an activating element (ACT) that contributes to RING2 release by mimicking RING2 interactions on the UPD, explaining further AR-JP mutations. Our data show how autoinhibition in parkin is resolved, and suggest a mechanism for how parkin ubiquitinates its substrates via an untethered RING2 domain. These findings open new avenues for the design of parkin activators for clinical use.

Multiscale enhanced sampling of glucokinase: Regulation of the enzymatic reaction via a large scale domain motion

Enhanced sampling yields a comprehensive structural ensemble or a free energy landscape, which is beyond the capability of a conventional molecular dynamics simulation. Our recently developed multiscale enhanced sampling (MSES) method employs a coarse-grained model coupled with the target physical system for the efficient acceleration of the dynamics. MSES has demonstrated applicability to large protein systems in solution, such as intrinsically disordered proteins and protein-protein and protein-ligand interactions. Here, we applied the MSES simulation to an important drug discovery target, glucokinase (GCK), to elucidate the structural basis of the positive cooperativity of the enzymatic reaction at an atomistic resolution. MSES enabled us to compare two sets of the free energy landscapes of GCK, for the glucose-bound and glucose-unbound forms, and thus demonstrated the drastic change of the free energy surface depending on the glucose concentration. In the glucose-bound form, we found two distinct basins separated by a high energy barrier originating from the domain motion and the folding/unfolding of the α13 helix. By contrast, in the glucose-unbound form, a single flat basin extended to the open and super-open states. These features illustrated the two distinct phases achieving the cooperativity, the fast reaction cycle staying in the closed state at a high glucose concentration and the slow cycle primarily in the open/super-open state at a low concentration. The weighted ensemble simulations revealed the kinetics of the structural changes in GCK with the synergetic use of the MSES results; the rate constant of the transition between the closed state and the open/super-open states, kC/O = 1.1 ms-1, is on the same order as the experimental catalytic rate, kcat = 0.22 ms-1. Finally, we discuss the pharmacological activities of GCK activators (small molecular drugs modulating the GCK activity) in terms of the slight changes in the domain motion, depending on their chemical structures as regulators. The present study demonstrated the capability of the enhanced sampling and the associated kinetic calculations for understanding the atomistic structural dynamics of protein systems in physiological environments.

Phase field analysis of crack tip parameters in ferroelectric polycrystals under large-scale switching

The determination of fracture parameters at cracks in ferroelectrics under large-scale domain switching is still a great challenge. In order to evaluate the crack-tip mechanical and electrical field intensity factors, the interaction integral (I-integral) technique is further developed to cope with the heterogeneous microstructures based on the polarization distribution and crack tip fields from phase field simulations. The enhanced I-integral exhibits several merits over previous techniques for determining the crack-tip intensity factors. First, small-scale switching assumption is unnecessary. Second, the intensity factors of different modes are decoupled. Third, it is independent of integration area size, regardless of the presence of grain boundaries and domain walls. These advantages ensure the successful application of the enhanced I-integral to study toughening effects in ferroelectric polycrystals due to large-scale domain switching. Using this approach, a tensile test of PbTiO3 ferroelectric polycrystals with an impermeable crack is simulated. Simulations show that domain switching initiates not only from the crack tip but also from the grain boundaries due to high polarization gradient and stress concentration. Large-scale switching triggered by a critical load reduces the crack-tip stress intensity factors anomalously. In comparison to single crystals, the critical load for polycrystals is lower and even vanishes due to grain orientations. The results also demonstrate that the I-integral method possesses satisfactory accuracy and good area-independence for grain boundaries and domain walls.

Sedimentary architecture, depositional facies and diagenetic response to intracratonic deformation and climate change inferred from outcrops for a pivotal period (Jurassic/Cretaceous boundary, Paris Basin, France)

The aim of this study is to decipher the respective influences of geodynamic and climate disturbances at the Jurassic/Cretaceous boundary on sedimentary facies and carbonate diagenesis in a stable intracratonic basin using isotopic geochemistry and subsidence quantification. Fourteen lithofacies were deposited in a (1) carbonate platform and (2) a delta plain environment. Climate change from cool and wet to warm and semi-arid conditions during the early Tithonian influenced the syn-sedimentary dolomitization process within the carbonate platform during the mid-Tithonian. Architecture and facies reconstructions well-constrained the Jurassic-Cretaceous Unconformity (JCU), which was an important local structural episode marked by (1) an 80 m uplift in the eastern Paris Basin and by (2) the formation of a NW–SE low wavelength 15 km-wide and 30 km-long flexure. This first tectonic event tended to maintain brine ponds and supratidal marsh environments in the platform during the late Tithonian and early Berriasian, forming Purbeckian facies and associated dolomitic facies. A major depositional change occurred between the early and late Berriasian from shallow carbonate platform environments to fluviatile-deltaic clastic deposits (Wealden facies). This facies change is underlain by a major unconformity corresponding to the Ryazanian unconformity. It is marked (1) by erosion processes, karstification of the carbonate substrate, and the development of ferruginous weathering products (goethite), followed by (2) incision processes in a fluvial-deltaic environment. This unconformity is consecutive to a 40 m uplift in the eastern Paris Basin. The rifting phase in the Bay of Biscay, in the Pyrenean Zone, and in the Artic-North Atlantic together with the opening of the Ligurian Sea had a major influence on the northern part of France by causing uplifts (120 m from the Tithonian) and flexuring. Geodynamics played a major role in carbonate demise in the Paris Basin leading to exposure and karstification of the carbonate platform. Added to the generalized uplift, western Tethyan cool and humid conditions from the late Berriasian caused terrigenous influx into large-scale marine domains which was detrimental and unfavorable to carbonate growth.