Spatial Rearrangement Research Articles

Cognition-related connectome gradient dysfunctions of thalamus and basal ganglia in drug-naïve first-episode major depressive disorder

BackgroundSubcortical functional abnormalities are believed to contribute to clinical symptoms and cognitive impairments in major depressive disorder (MDD). By introducing functional gradient mapping, the present study evaluated subcortical gradients in MDD patients and their association with cognitive features. MethodsOrganization patterns and between-group differences in the principal subcortical gradient were investigated in 145 never-treated first-episode MDD patients and 145 healthy controls (HCs) across limbic, thalamic, and basal ganglia (BG) systems and their structural and functional subregions. We also assessed the associations between significant gradient alterations and clinical characteristics and neuropsychological functioning. ResultsOverall, MDD patients showed a relatively compressed and disturbed gradient organization than HCs, with limbic and BG regions located at the two extreme ends of the principal gradient. Specifically, MDD patients had lower principal gradient values in thalamus and limbic system but higher values in BG than HCs. These gradient alterations, associated with intrinsic Euclidian distance and functional connectivity patterns, manifested as spatial rearrangements of gradient values within each respective subregion. Lower gradient values in thalamic subregion projecting to default mode network were associated with higher principal gradient values in BG subregion projecting to ventral attention network, and these gradient alterations were correlated with poorer episodic memory performance in MDD patients. LimitationsThe specific neuropathological mechanisms driving the gradient alterations still require further investigation. ConclusionsOpposing gradient alterations in the thalamic and BG regions synergistically impact episodic memory performance in MDD, revealing an internally differentiated and cognition related pattern of subcortical gradient dysfunction in MDD.

Dissecting glial scar formation by spatial point pattern and topological data analysis

Glial scar formation represents a fundamental response to central nervous system (CNS) injuries. It is mainly characterized by a well-defined spatial rearrangement of reactive astrocytes and microglia. The mechanisms underlying glial scar formation have been extensively studied, yet quantitative descriptors of the spatial arrangement of reactive glial cells remain limited. Here, we present a novel approach using point pattern analysis (PPA) and topological data analysis (TDA) to quantify spatial patterns of reactive glial cells after experimental ischemic stroke in mice. We provide open and reproducible tools using R and Julia to quantify spatial intensity, cell covariance and conditional distribution, cell-to-cell interactions, and short/long-scale arrangement, which collectively disentangle the arrangement patterns of the glial scar. This approach unravels a substantial divergence in the distribution of GFAP+ and IBA1+ cells after injury that conventional analysis methods cannot fully characterize. PPA and TDA are valuable tools for studying the complex spatial arrangement of reactive glia and other nervous cells following CNS injuries and have potential applications for evaluating glial-targeted restorative therapies.

The Assessment of Upper Airway Volume Changes Following Bimaxillary Advancement Surgery: A Radiological Evaluation in the Supine Position at Multiple Intervals.

Background: Bimaxillary surgeries (BiMax) are an essential part of the craniomaxillofacial specialty. The osteotomies and subsequent spatial rearrangement of the maxilla and the mandible enable the correction of facial deformities, asymmetry, and malocclusion. Moreover, the movements performed during the procedure affect the morphology of surrounding soft tissues, including the upper airway (UA). Objectives: The objective of this study was to radiologically assess the potential volumetric alterations of the UA in the supine position at various intervals following BiMax advancement surgeries. Methods: A group of 31 patients who underwent BiMax advancement surgery were included in the study. Medical computed tomography (CT) of the head and neck region was performed 2 weeks preoperatively, 1 day postoperatively, and 6 months postoperatively. The UA volumes were calculated and analyzed based on the acquired Digital Imaging and Communications in Medicine (DICOM) files using different software applications. The sella-nasion-A point (SNA) and sella-nasion-B point (SNB) angles were evaluated to measure the achieved maxillomandibular advancement. Results: When comparing the volume of the UA before surgery, post-surgery, and 6 months post-surgery, the p-value was <0.001, indicating statistically significant differences in UA volume between the successive examinations. A statistically significant difference was found between UA volume before surgery and 6 months post-surgery and between UA volume after surgery and 6 months post-surgery, with the obtained p-values being <0.001 and 0.001, respectively. A significantly larger UA volume was observed 6 months post-surgery (mean ± SD: 27.3 ± 7.3) compared to the volume before surgery (mean ± SD: 22.2 ± 6.4), as well as 6 months post-surgery compared to the volume assessed shortly after surgery (mean ± SD: 24.2 ± 7.3). Conclusions: BiMax advancement surgeries result in the significant enlargement of the UA. The volume of the UA does not diminish immediately following the procedure and is not constant; it increases significantly during the postoperative observation period.

Unveiling nuclear chromatin distribution using IsoConcentraChromJ: A flourescence imaging plugin for IsoRegional and IsoVolumetric based ratios analysis.

Chromatin exhibits non-random distribution within the nucleus being arranged into discrete domains that are spatially organized throughout the nuclear space. Both the spatial distribution and structural rearrangement of chromatin domains in the nucleus depend on epigenetic modifications of DNA and/or histones and structural elements such as the nuclear envelope. These components collectively contribute to the organization and rearrangement of chromatin domains, thereby influencing genome architecture and functional regulation. This study develops an innovative, user-friendly, ImageJ-based plugin, called IsoConcentraChromJ, aimed quantitatively delineating the spatial distribution of chromatin regions in concentric patterns. The IsoConcentraChromJ can be applied to quantitative chromatin analysis in both two- and three-dimensional spaces. After DNA and histone staining with fluorescent probes, high-resolution images of nuclei have been obtained using advanced fluorescence microscopy approaches, including confocal and stimulated emission depletion (STED) microscopy. IsoConcentraChromJ workflow comprises the following sequential steps: nucleus segmentation, thresholding, masking, normalization, and trisection with specified ratios for either 2D or 3D acquisitions. The effectiveness of the IsoConcentraChromJ has been validated and demonstrated using experimental datasets consisting in nuclei images of pre-adipocytes and mature adipocytes, encompassing both 2D and 3D imaging. The outcomes allow to characterize the nuclear architecture by calculating the ratios between specific concentric nuclear areas/volumes of acetylated chromatin with respect to total acetylated chromatin and/or total DNA. The novel IsoConcentrapChromJ plugin could represent a valuable resource for researchers investigating the rearrangement of chromatin architecture driven by epigenetic mechanisms using nuclear images obtained by different fluorescence microscopy methods.

Confined Ionic Environments Tailoring the Reactivity of Molecules in the Micropores of BEA-Type Zeolite.

In the presence of water, hydronium ions formed within the micropores of zeolite H-BEA significantly influence the surrounding environment and the reactivity of organic substrates. The positive charge of these ions, coupled with the zeolite's negatively charged framework, results in an ionic environment that causes a strongly nonideal solvation behavior of cyclohexanol. This leads to a significantly higher excess chemical potential in the initial state and stabilizes at the same time the charged transition state in the dehydration of cyclohexanol. As a result, the free-energy barrier of the reaction is lowered, leading to a marked increase in the reaction rates. Nonetheless, there is a limit to the reaction rate enhancement by the hydronium ion concentration. Experiments conducted with low concentrations of reactants show that beyond an optimal concentration, the required spatial rearrangement between hydronium ions and cyclohexanols inhibits further increases in the reaction rate, leading to a peak in the intrinsic activity of hydronium ions. The quantification of excess chemical potential in both initial and transition states for zeolites H-BEA, along with findings from HMFI, provides a basis to generalize and predict rates for hydronium-ion-catalyzed dehydration reactions in Brønsted zeolites.

Modeling phase separation and composition patterning in FeCrAl alloys at neutron irradiation

Possible scenarios of the microstructural evolution of FeCrAl alloys under neutron irradiation are studied by using the phase-field method. The exploited approach is generalized by considering ballistic mixing of atoms, spatial rearrangement of point defects, and dynamics of their sinks (dislocation loops), self-consistently. Stability diagrams manifesting domains of main control parameters (irradiation temperature, damage rate, atomic relocation distance) governing precipitation are obtained. It is shown that depending on irradiation conditions a precipitation of the Cr-rich α′ -phase proceeds by either phase decomposition or composition patterning mechanism. Statistical analysis of precipitation kinetics is provided by studying precipitate number density, mean precipitate size and Chromium content in α′ -phase for a model alloy Fe-30%Cr-5%Al. A locality of point defects distribution with high concentration and dislocation loops growth are discussed. The hardening change is estimated for two possible scenarios of precipitation. Obtained results are verified with experimental observations. This study provides a deep insight into details of microstructural transformation in FeCrAl alloys during neutron irradiation.

Nail Telocytes: Identification, Potential Physiological Function, and Role in Pathology: A Reappraisal of the So-Called Onychofibroblasts/Onychodermis.

Some authors have suggested that the fibroblasts of the nail mesenchyme (onychofibroblasts) can be distinguished from skin fibroblasts by their high expression of CD10. My 2015 study documented the presence of a relatively sparse CD34 + /CD10 + dendritic subpopulation in the dermis and hypodermis of the matrix. For some time now, my hypothesis has been that these interstitial dendritic mesenchymal cells of the matrix correspond to telocytes. Telocytes have been described as peculiar interstitial dendritic cells present in the mesenchymal tissue of numerous organs, including the skin, but their presence and characteristics in the nail unit have not been explored. This study was undertaken to more comprehensively investigate the existence and characteristics of nail telocytes. A series of 20 normal adult nail units were examined with a combination of morphological and immunohistochemical analyses. The matrix dermis contained a sparse subpopulation of CD34 + /CD10 + elongated telocytes with a higher density in the lunular region and, at this distal level, a change in their immunohistochemical profile, resulting in a progressive loss of CD34 expression. The matrix hypodermis showed CD34 + /CD10 + telocytes in their classical elongated aspect, which acquired, especially in the distal fibromyxoid area of the thumb, an oval to round morphology with multiple intracytoplasmic vacuoles. The characteristic dynamic immunophenotypic profile of the dermal telocytes with a progressive distal loss of the defining molecule CD34 was equally observed in the distal hypodermis. The nail bed dermis was thick with a dense fibrous connective tissue. A reticular network of CD34 - /CD10 + telocytes was present in the superficial dermis of the proximal nail bed. The mesenchymal cells of the deep part of the proximal nail bed dermis and the entire distal nail bed dermis were CD34 - /CD10 - . The adult nail mesenchyme is composed of 3 microanatomically distinct regions. Only the thumb has a distal hypodermis rich in mucinous material. The population of telocytes is relatively sparse compared with the fibroblastic population of the entire nail mesenchyme. The concept of onychodermis/onychofibroblasts is not valid. Nail telocytes have a dynamic immunohistochemical profile depending on whether they are located proximally or distally. The CD34 + /CD10 + profile correlates with the onychogenic epithelial region, while the CD34 - /CD10 + profile correlates with a spatial rearrangement of the nail epidermal bed.

Some aspects of the resistive-to-normal state transition caused by direct and microwave currents in superconducting thin films with phase slip lines

Based on analysis of current-voltage characteristics and imaging of the resistive state of thin-film tin strips using low-temperature laser scanning microscopy (LTLSM), the process of destruction of superconductivity by current and microwave irradiation with the formation and spatial rearrangement of the order parameter phase slip lines, and their transformation into discrete localized normal domains are shown. The prospects of LTLSM are considered from the point of view of the study of the high-frequency properties of superconducting structures and spatial characteristics in the pre-critical state for instrumental applications.

Deformable polarization singularity array by superimposed Ince–Gaussian beams

We present a numerical and experimental study of polarization singularity arrays, which are generated by the coherent superposition of orthogonal, linearly polarized, even and odd Ince–Gaussian (IG) beams. The generated array consists of multiple polarization singularities of different types. The type of the polarization singularities can be adjusted effectively by switching the linear polarization states of two IG modes and by modifying the relative phase factor. In addition, we study the evolution of the arrays with the ellipticity parameter, which leads to the splitting and spatial rearrangement of polarization singularities. This work may have implications for material processing, optical trapping, and manipulation.

Understanding the molecular mechanism of pathogenic variants of BIR2 domain in XIAP-deficient inflammatory bowel disease

X-linked inhibitor of apoptosis protein (XIAP) deficiency causes refractory inflammatory bowel disease. The XIAP protein plays a pivotal role in the pro-inflammatory response through the nucleotide-binding oligomerization domain-containing signaling pathway that is important in mucosal homeostasis. We analyzed the molecular mechanism of non-synonymous pathogenic variants (PVs) of XIAP BIR2 domain. We generated N-terminally green fluorescent protein-tagged XIAP constructs of representative non-synonymous PVs. Co-immunoprecipitation and fluorescence cross-correlation spectroscopy showed that wild-type XIAP and RIP2 preferentially interacted in live cells, whereas all non-synonymous PV XIAPs failed to interact properly with RIP2. Structural analysis showed that various structural changes by mutations, such as hydrophobic core collapse, Zn-finger loss, and spatial rearrangement, destabilized the two loop structures (174–182 and 205–215) that critically interact with RIP2. Subsequently, it caused a failure of RIP2 ubiquitination and loss of protein deficiency by the auto-ubiquitination of all XIAP mutants. These findings could enhance our understanding of the role of XIAP mutations in XIAP-deficient inflammatory bowel disease and may benefit future therapeutic strategies.

An Efficient Multiscale Spatial Rearrangement MLP Architecture for Image Restoration.

The effective use of long-range information can yield improved network performance, which is very important for image restoration. Although local window-based models have linear complexity and can be feasibly applied to process high-resolution images, a single-scale window has a limited receptive field and is less efficient for encoding long-range context information. To address this issue, this paper presents a single-stage multiscale spatial rearrangement multilayer perceptron (MSSR-MLP) architecture that can obtain information at different scales within a local window. Specifically, we propose a simple and efficient spatial rearrangement module (SRM) that moves information outside the local window to the inside of the local window so that long-range dependencies can be modeled using only a window-based fully connected (FC) layer. The SRM can extend the local receptive field of a window-based FC layer without introducing additional parameters and FLOPs. Utilizing several spatial rearrangement modules with different step sizes, we design an efficient multiscale spatial rearrangement MLP architecture for image restoration. This design aggregates multiscale information to achieve improved restoration quality while maintaining a low computational cost. Extensive experiments conducted on several image restoration tasks demonstrate the efficiency and effectiveness of our method. For example, it requires only ~4.3% of the FLOPs needed by SwinIR for Gaussian gray image denoising, ~13.9% of the FLOPs needed by C2 PNet for single-image dehazing and ~18.9% of the FLOPs needed by MAXIM for single-image motion deblurring but achieves better performance on each of these restoration tasks.

Improving the formability and mechanical properties of TiAl alloy by direct forging of uncondensed powder

The limited plasticity and poor formability of TiAl alloys constitute primary constraints on their widespread applicability. In this regard, an innovative forming method is proposed, characterized by the direct forging of unconsolidated pre-alloyed Ti–48Al–2Cr–2Nb powders. In this procedure, spherical powders with a broad particle size distribution are pre-encapsulated and subjected to vacuumed treatment, followed by direct high-temperature forging to attain the final desired shape. Throughout the process, the powders undergo pre-heating to various forming temperatures and are forged at different speeds, enabling a comparative analysis of the effect of forging temperature and speed on densification and the microstructural characteristics of the forged billet. Experimental results indicate that the powders can be nearly fully densified when direct forging is conducted within the α-phase region. By combining the finite element modeling and microstructural characterization, three mechanisms dominating the consolidation process of powders are revealed. Initial particle clustering and spatial rearrangement predominantly occur during the early deformation stage, enhancing densification. Subsequent fragmentation of particles, induced by severe plastic deformation, governs the entire deformation process, leading to the elimination of the prior particle boundaries and substantial densification improvement. The closure of the micrometer-scale voids is controlled by high-temperature diffusion and creep, which plays a pivotal role in weakening the detrimental effect of micro defects on mechanical properties. The above mechanisms act alternately or simultaneously, resulting in a homogeneous microstructure composed of α2+γ lamellae and bulk γ with small sizes, and a good synergy of strength and ductility. Therefore, this novel approach holds considerable potential as a cost-effective alternative strategy for producing TiAl components.

Spatial Rearrangement of Manufacturing Industrial Zones Based on MCDM in Mojokerto Regency. Case Study Northern Mojokerto Region

Mojokerto Regency is part of the national strategic area (Gerbangkertasusila) in East Java. Gerbangkertasusila serves as the driving force behind East Java’s economy, with the manufacturing industry becoming the prime mover as it contributes to 2022 GRDP by 56.68 percent. The spatial plan of Mojokerto Regency includes the development of an industrial estate in the northern part, specifically in Jetis and Dawarblandong Districts, covering a total area of 8.553 hectares. However, the government’s attempt to make industrial estates has only been realized by 2.65% since 2012. This research aims to assess the suitability of space allocation within the industrial estates in the northern region of Mojokerto. The research method uses spatial analysis approach, multi criteria decision making (MCDM). Spatial data were obtained through RBI and Bhumi ATR, also Mojokerto Regency’s RTRW as comparative data to assess the suitability of industrial locations. This study also considers other spatial aspects, such as projections of land use based on cellular automata, population, infrastructure, transportation, and physical conditions. Analysis result shows that the allocation of space requirements for industrial estate development is 1,081 hectares or 12.64 percent of the original plan. The area is much smaller than the planned area in the Mojokerto Regency’s RTRW. The study identifies four potential locations for Industrial Estate development in the northern Mojokerto region, consisting of two in Jetis District and two in Dawarblandong District. The research results can be an input for the industrial cluster development in the northern Mojokerto region.

Seasonal rearrangements in the use of coastal habitat mosaics by tropical fishes create a cyclic functional trajectory

Coastal habitat mosaics are among the most productive ecosystem on earth, having important functions for fish species throughout their life cycle. The complex dynamic of these areas, marked by constant changes in environmental conditions, creates spatial and temporal rearrangements of assemblages that may have significant impacts on ecosystem functioning. Thus, this study aimed to assess how seasonal variations in species composition affect the diversity of functions in these areas. We identified functional guilds of fish species found in three coastal habitat mosaics and used their functional traits as indicators of ecosystem functionality. Our results demonstrated that coastal habitat mosaics exhibit significant spatial and temporal variations in both, guilds, and functions, with remarkable differences in between-habitat responses to the onset of the tropical rainy season. More specifically, we found that mangroves exhibit a clear linear relationship between rainfall and functions, whereas in seagrass beds, functional diversity increases at low levels of rainfall and decreases at high levels. Lastly, sandy beaches have its functions increased by rainfall, but reaches an asymptote. These patterns point out to habitat-specific functional trajectories through time, which can be explained by the movements of species through the coastal mosaic in response to environmental variability, and to ontogenetic migration as species grow.

Practical Solutions to Enhance the Productivity of Waste Picker Organizations Through the Application of Lean Tools

Purpose: The aim of the research is to improve the productivity of a Waste Picker Organization using lean tools. Introduction: Waste Pickers Organizations (WPO) play a key role in the circular economy and in the Brazilian recycling industry, but several organizational structure inefficiencies hamper productivity. One way to understand how these inefficiencies occur and how to eliminate them is through the application of Lean thinking. Methodology: Lean tools (SIPOC, process modelling, Value Stream Mapping, spaghetti diagram, activity value analysis, and spatial rearrangement) were explored for the analysis of operational activities, focusing on elimination of unnecessary activities and layout changes, and to measure the improvements. Results and Conclusion: After the implementation of the suggested improvements in the WPO waste selection macro process, several productivity enhancements were noted, including a reduction of initial stock (59%), a decreased lead time (41%), lower processing times (57%), and improved cargo handling (17%). These findings clearly indicate how the application of lean tools can improve overall productivity in Waste Picker Organizations being practical solutions that only require human resource. Research implications: Lean tools to enhance the productivity of WPO were applied as practical and inexpensive solutions to identify and describe the main flows and layout types at Waste Picker Organizations (WPO). Originality/value: Practical solutions are the most request issues regarding improvement actions implementations in waste management, but especially when the focus is the waste picker organizations due to the government's financial dependence as the main economic source and difficulties in self-management.

Molecular Design of FRET Probes Based on Domain Rearrangement of Protein Disulfide Isomerase for Monitoring Intracellular Redox Status.

Multidomain proteins can exhibit sophisticated functions based on cooperative interactions and allosteric regulation through spatial rearrangements of the multiple domains. This study explored the potential of using multidomain proteins as a basis for Förster resonance energy transfer (FRET) biosensors, focusing on protein disulfide isomerase (PDI) as a representative example. PDI, a well-studied multidomain protein, undergoes redox-dependent conformational changes, enabling the exposure of a hydrophobic surface extending across the b' and a' domains that serves as the primary binding site for substrates. Taking advantage of the dynamic domain rearrangements of PDI, we developed FRET-based biosensors by fusing the b' and a' domains of thermophilic fungal PDI with fluorescent proteins as the FRET acceptor and donor, respectively. Both experimental and computational approaches were used to characterize FRET efficiency in different redox states. In vitro and in vivo evaluations demonstrated higher FRET efficiency of this biosensor in the oxidized form, reflecting the domain rearrangement and its responsiveness to intracellular redox environments. This novel approach of exploiting redox-dependent domain dynamics in multidomain proteins offers promising opportunities for designing innovative FRET-based biosensors with potential applications in studying cellular redox regulation and beyond.

Chiral flows can induce neck formation in viscoelastic surfaces

The cell cortex is an active viscoelastic self-deforming sheet at the periphery of animal cells. It constricts animal cells during cell division. For some egg cells, the actomyosin cortex was shown to exhibit counter-rotating chiral flows along the axis of division. Such chiral surface flows were shown to contribute to spatial rearrangements and left-right symmetry breaking in developing organisms. In spite of this prospective biological importance, the effect of chiral forces on the flows and emergent shape dynamics of a deformable surface are completely unknown. To shed a first light on that matter, we present here a numerical study of an axisymmetric viscoelastic surface embedded in a viscous fluid. We impose a generic counter-rotating force field on this surface and study the resulting chiral flow field and shape dynamics for various surface mechanical parameters. Notably, we find that the building of a neck, as is observed during cell division, occurs if the surface contains a strong shear elastic component. Furthermore, we find that a large areal relaxation time results in flows towards the equator of the surface. These flows assist the transport of a surface concentration during the formation of a contractile ring. Accordingly, we show that chiral forces by themselves can drive pattern formation and stabilise contractile rings at the equator. These results provide first mechanistic evidence that chiral flows can play a significant role to orchestrate cell division.

Interfacial engineered superelastic metal-organic framework aerogels with van-der-Waals barrier channels for nerve agents decomposition

Chemical warfare agents (CWAs) significantly threaten human peace and global security. Most personal protective equipment (PPE) deployed to prevent exposure to CWAs is generally devoid of self-detoxifying activity. Here we report the spatial rearrangement of metal-organic frameworks (MOFs) into superelastic lamellar-structured aerogels based on a ceramic network-assisted interfacial engineering protocol. The optimized aerogels exhibit efficient adsorption and decomposition performance against CWAs either in liquid or aerosol forms (half-life of 5.29 min, dynamic breakthrough extent of 400 L g−1) due to the preserved MOF structure, van-der-Waals barrier channels, minimized diffusion resistance (~41% reduction), and stability over a thousand compressions. The successful construction of the attractive materials offers fascinating perspectives on the development of field-deployable, real-time detoxifying, and structurally adaptable PPE that could be served as outdoor emergency life-saving devices against CWAs threats. This work also provides a guiding toolbox for incorporating other critical adsorbents into the accessible 3D matrix with enhanced gas transport properties.

Inside Out Computational Redesign of Cavities for Improving Thermostability and Catalytic Activity of Rhizomucor Miehei Lipase.

Cavities are created by hydrophobic interactions between residue side chain atoms during the folding of enzymes. Redesigning cavities can improve the thermostability and catalytic activity of the enzyme; however, the synergistic effect of cavities remains unclear. In this study, Rhizomucor miehei lipase (RML) was used as a model to explore volume fluctuation and spatial distribution changes of the internal cavities, which could reveal the roles of internal cavities in the thermostability and catalytic activity. We present an inside out cavity engineering (CE) strategy based on computational techniques to explore how changes in the volumes and spatial distribution of cavities affect the thermostability and catalytic activity of the enzyme. We obtained 12 single-point mutants, among which the melting temperatures (Tm) of 8 mutants showed an increase of more than 2°C. Sixteen multipoint mutations were further designed by spatial distribution rearrangement of internal cavities. The Tm of the most stable triple variant, with mutations including T21V (a change of T to V at position 21), S27A, and T198L (T21V/S27A/T198L), was elevated by 11.0°C, together with a 28.7-fold increase in the half-life at 65°C and a specific activity increase of 9.9-fold (up to 5,828 U mg-1), one of the highest lipase activities reported. The possible mechanism of decreased volumes and spatial rearrangement of the internal cavities improved the stability of the enzyme, optimizing the outer substrate tunnel to improve the catalytic efficiency. Overall, the inside out computational redesign of cavities method could help to deeply understand the effect of cavities on enzymatic stability and activity, which would be beneficial for protein engineering efforts to optimize natural enzymes. IMPORTANCE In the present study, R. miehei lipase, which is widely used in various industries, provides an opportunity to explore the effects of internal cavities on the thermostability and catalytic activity of enzymes. Here, we execute high hydrostatic pressure molecular dynamics (HP-MD) simulations to screen the critical internal cavity and reshape the internal cavities through site-directed mutation. We show that as the global internal cavity volume decreases, cavity rearrangement can improve the stability of the protein while optimizing the substrate channel to improve the catalytic efficiency. Our results provide significant insights into understanding the mechanism of action of the internal cavity. Our strategy is expected to be applied to other enzymes to promote increases in thermostability and catalytic activity.

The binding mode of orphan glycyl-tRNA synthetase with tRNA supports the synthetase classification and reveals large domain movements.

As a class of essential enzymes in protein translation, aminoacyl-transfer RNA (tRNA) synthetases (aaRSs) are organized into two classes of 10 enzymes each, based on two conserved active site architectures. The (αβ)2 glycyl-tRNA synthetase (GlyRS) in many bacteria is an orphan aaRS whose sequence and unprecedented X-shaped structure are distinct from those of all other aaRSs, including many other bacterial and all eukaryotic GlyRSs. Here, we report a cocrystal structure to elucidate how the orphan GlyRS kingdom specifically recognizes its substrate tRNA. This structure is sharply different from those of other aaRS-tRNA complexes but conforms to the clash-free, cross-class aaRS-tRNA docking found with conventional structures and reinforces the class-reconstruction paradigm. In addition, noteworthy, the X shape of orphan GlyRS is condensed with the largest known spatial rearrangement needed by aaRSs to capture tRNAs, which suggests potential nonactive site targets for aaRS-directed antibiotics, instead of less differentiated hard-to-drug active site locations.