Perspectives on label-free microscopy of heterogeneous and dynamic biological systems.

Significance: Advancements in label-free microscopy could provide real-time, non-invasive imaging with unique sources of contrast and automated standardized analysis to characterize heterogeneous and dynamic biological processes. These tools would overcome challenges with widely used methods that are destructive (e.g., histology, flow cytometry) or lack cellular resolution (e.g., plate-based assays, whole animal bioluminescence imaging). Aim: This perspective aims to (1) justify the need for label-free microscopy to track heterogeneous cellular functions over time and space within unperturbed systems and (2) recommend improvements regarding instrumentation, image analysis, and image interpretation to address these needs. Approach: Three key research areas (cancer research, autoimmune disease, and tissue and cell engineering) are considered to support the need for label-free microscopy to characterize heterogeneity and dynamics within biological systems. Based on the strengths (e.g., multiple sources of molecular contrast, non-invasive monitoring) and weaknesses (e.g., imaging depth, image interpretation) of several label-free microscopy modalities, improvements for future imaging systems are recommended. Conclusion: Improvements in instrumentation including strategies that increase resolution and imaging speed, standardization and centralization of image analysis tools, and robust data validation and interpretation will expand the applications of label-free microscopy to study heterogeneous and dynamic biological systems.

Preparation of magnetic activated carbon fibers@Fe3O4 by electrostatic self-assembly method and adsorption properties for methylene blue.

Nano-Fe3O4 was loaded onto coconut-based activated carbon fibres (CACF) using an electrostatic self-assembly method. The effects of the mass ratio of CACF to nano-Fe3O4, loading time, pH and temperature on the loading effect were investigated and ideal loading conditions were determined. To study the adsorption performance of MACF@Fe3O4 for methylene blue, the effects of the initial concentration, pH and time on the adsorption were investigated and the working conditions of adsorption were established. MACF@Fe3O4 was systematically characterized. Adsorption kinetics were investigated under ideal conditions. The ideal loading conditions for MACF@Fe3O4 were as follows: mass ratio of 1:1, 20 min, pH 9.36, 22.5°C. The saturation magnetization of MACF@Fe3O4 was 48.2263 emu·g-1, which could be quickly separated under an external magnetic field. When the dosage was 0.010 g, the adsorption rate reached 97.29% and the maximum adsorption capacity was 12.1616 mg·g-1. The adsorption process conformed to pseudo-first-order kinetics during the first 15 min and pseudo-second-order kinetics during 20-120 min. The equations were ln( Q e - Q t )=2.2394-0.0689t and t Q t =0.0774 + 0.5295t , respectively. The isothermal adsorption model showed that MACF@Fe3O4 was more in line with the Langmuir model, indicating that the adsorption process was mainly monolayer adsorption. The thermodynamic analysis results showed that the adsorption process of MB by MACF@Fe3O4 was an endothermic process. In this study, MACF@Fe3O4 with high adsorption capacity and easy separation from coconut palm fibres has good application prospects in the field of adsorption, which can promote the high-value utilization of coconut palms.

Cheminformatics-based identification of phosphorylated RET tyrosine kinase inhibitors for human cancer.

Background: Rearranged during transfection (RET), an oncogenic protein, is associated with various cancers, including non-small-cell lung cancer (NSCLC), papillary thyroid cancer (PTC), pancreatic cancer, medullary thyroid cancer (MTC), breast cancer, and colorectal cancer. Dysregulation of RET contributes to cancer development, highlighting the importance of identifying lead compounds targeting this protein due to its pivotal role in cancer progression. Therefore, this study aims to discover effective lead compounds targeting RET across different cancer types and evaluate their potential to inhibit cancer progression. Methods: This study used a range of computational techniques, including Phase database creation, high-throughput virtual screening (HTVS), molecular docking, molecular mechanics with generalized Born surface area (MM-GBSA) solvation, assessment of pharmacokinetic (PK) properties, and molecular dynamics (MD) simulations, to identify potential lead compounds targeting RET. Results: Initially, a high-throughput virtual screening of the ZINC database identified 2,550 compounds from a pool of 170,269. Subsequent molecular docking studies revealed 10 compounds with promising negative binding scores ranging from -8.458 to -7.791 kcal/mol. MM-GBSA analysis further confirmed the potential of four compounds to exhibit negative binding scores. MD simulations demonstrated the stability of CID 95842900, CID 137030374, CID 124958150, and CID 110126793 with the target receptors. Conclusion: These findings suggest that these selected four compounds have the potential to inhibit phosphorylated RET (pRET) tyrosine kinase activity and may represent promising candidates for the treatment of various cancers.

New insights into the role of mitochondrial dynamics in oxidative stress-induced diseases.

The accumulation of excess reactive oxygen species (ROS) can lead to oxidative stress (OS), which can induce gene mutations, protein denaturation, and lipid peroxidation directly or indirectly. The expression is reduced ATP level in cells, increased cytoplasmic Ca2+, inflammation, and so on. Consequently, ROS are recognized as significant risk factors for human aging and various diseases, including diabetes, cardiovascular diseases, and neurodegenerative diseases. Mitochondria are involved in the production of ROS through the respiratory chain. Abnormal mitochondrial characteristics, including mitochondrial OS, mitochondrial fission, mitochondrial fusion, and mitophagy, play an important role in various tissues. However, previous excellent reviews focused on OS-induced diseases. In this review, we focus on the latest progress of OS-induced mitochondrial dynamics, discuss OS-induced mitochondrial damage-related diseases, and summarize the OS-induced mitochondrial dynamics-related signaling pathways. Additionally, it elaborates on potential therapeutic methods aimed at preventing oxidative stress from further exacerbating mitochondrial disorders.

Mining and characterization of novel antimicrobial peptides from the large-scale microbiome of Shanxi aged vinegar based on metagenomics, molecular dynamics simulations and mechanism validation.

The study aimed to mine and characterize novel antimicrobial peptides (AMPs) from the Shanxi aged vinegar microbiome. Utilizing machine learning techniques, AlphaFold2 structure prediction and molecular dynamics simulations, six novel AMPs were innovatively mined from 98,539 peptides based on metagenomic data, of which one peptide secreted by Lactobacillus (named La-AMP) was experimentally validated to have remarkable bactericidal effects against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) with high stability and no hemolytic activity. Scanning electron microscopy revealed that La-AMP caused irreversible damage to cell membranes of S. aureus and E. coli, a finding further confirmed by calcein-AM/propidium iodide staining. Additionally, La-AMP induced nucleic acid leakage and reactive oxygen species accumulation in bacterial cells. It was found to bind to DNA gyrase through salt bridges, hydrogen bonds, and hydrophobic interactions, ultimately inducing apoptosis. Thus, La-AMP exhibited encouraging promise as a valuable bioactive component for the development of natural preservatives.

DN-ODE: Data-driven neural-ODE modeling for breast cancer tumor dynamics and progression-free survivals.

Pharmacokinetic/Pharmacodynamic (PK/PD) modeling is crucial in the development of new drugs. However, traditional population-based PK/PD models encounter challenges when modeling for individual patients. We aim to explore the potential of constructing a pharmacodynamic model for individual breast cancer pharmacodynamics leveraging only limited data from early clinical trial phases. While previous studies on Neural Ordinary Differential Equations (ODEs) suggest promising results in clinical trial practices, they primarily focused on theoretical applications or independent PK/PD modeling. PD modeling from complex and irregular clinical trial data, especially when interacting with PK parameters, is still unclear. To achieve that, we introduce a Data-driven Neural Ordinary Differential Equation (DN-ODE) modeling for breast cancer tumor dynamics and progression-free survival data. To validate this approach, experiments are conducted with early-phase clinical trial data from the Amcenestrant (an oral treatment for breast cancer) dataset (AMEERA 1-2), aiming to predict pharmacodynamics in the later phase (AMEERA 3). DN-ODE model achieves RMSE scores of 8.78 and 0.21 in tumor size and progression-free survival, respectively, with R2 scores over 0.9 for each task. Compared to PK/PD methodologies, DN-ODE is able to predict robust individual tumor dynamics with only limited cycle data. We also introduce Principal Component Analysis visualizations for encoder results, demonstrating the DN-ODE's capability to discern individual distributions and diverse tumor growth patterns. Therefore, DN-ODE facilitates comprehensive drug efficacy assessments, pinpoints potential responders, and aids in trial design.

On the dual role of (+)-catechin as primary antioxidant and inhibitor of viral proteases.

Natural antioxidants have become the subject of many investigations due to the role that they play in the reduction of oxidative stress. Their main scavenging mechanisms concern the direct inactivation of free radicals and the coordination of metal ions involved in Fenton-like reactions. Recently, increasing attention has been paid to non-covalent inhibition of enzymes involved in different diseases by the antioxidants. Here, a computational investigation on the primary antioxidant power of (+)-catechin against the •OOH radical has been performed in both lipid-like and aqueous environments, taking into account the relevant species present in the simulated acid-base equilibria at the physiological pH. Hydrogen Atom Transfer (HAT), Single Electron Transfer (SET), and Radical Adduct Formation (RAF) mechanisms were studied, and relative rate constants were estimated. The potential inhibitory activity of the (+)-catechin towards the most important proteases from SARS-CoV-2, 3C-like (Mpro) and papain-like (PLpro) proteases was also investigated by MD simulations to provide deeper atomistic insights on the binding sites. Based on the antioxidant and antiviral properties also unravelled by comparison with other molecules having similar chemical scaffold, our results propose that (+)-CTc satisfies can explicate a dual action as antioxidant and antiviral in particular versus Mpro from SARS-CoV-2.

Intrinsic dynamics of emulsions: Experiments in microgravity on the International Space Station.

HYPOTHESIS: In order to understand the basic mechanisms affecting emulsion stability, the intrinsic dynamics of the drop population must be investigated. We hypothesize that transient ballistic motion can serve as a marker of interactions between drops. In 1G conditions, buoyancy-induced drop motion obscures these interactions. The microgravity condition onboard the International Space Station enable this investigation. EXPERIMENTS: We performed Diffusing Wave Spectroscopy (DWS) experiments in the ESA Soft Matter Dynamics (SMD) facility. We used Monte Carlo simulations of photon trajectory to support data analysis. The analysis framework was validated by ground-based characterizations of the initial drop size distribution (DSD) and the properties of the oil/water interface in the presence of surfactant. FINDINGS: We characterized the drop size distribution and found to be bi-disperse. Drop dynamics shows transient ballistic features at early times, reaching a stationary regime of primarily diffusion-dominated motion. This suggests different ageing mechanisms: immediately after emulsification, the main mechanism is coalescence or aggregation between small drops. However at later times, ageing proceeds via coalescence or aggregation of small with large drops in some emulsions. Our results elucidate new processes relevant to emulsion stability with potential impact on industrial processes on Earth, as well as enabling technologies for space exploration.

Differential contribution of microbial and plant-derived organic matter to soil organic carbon sequestration over two decades of natural revegetation and cropping.

Both natural revegetation and cropping have great impact on long-term soil carbon (C) sequestration, yet the differences in their underlying mechanisms remain unclear. In this study, we investigated trends in soil organic C (SOC) accumulation during natural revegetation (VR) and cropping processes over 24 years, and explored the contributions of microbial necromass and plant-derived C to SOC formation and their primary controls. Over the course of 24 years of land use/cover change (LUCC) from 1995, SOC content exhibited a more substantial increase in VR (0.31 g kg-1 a-1) than in cropland (0.14 g kg-1 a-1) during Stage II (>10 y after LUCC), and recalcitrant organic carbon explained more of the SOC variation than easily oxidizable carbon. The higher SOC content in VR was attributed to a greater contribution of plant-derived C (14-28 %) than that in cropland (3-11 %) to SOC and a consistently lower ratio of cinnamyl (C)- to vanillyl (V)-type phenols in VR across all the assessed years. Although there were higher proportion of microbial necromass of SOC (41-84 %) in cropland than in VR, the differences were not significant. The dominant bacterial phylum of Chloroflexi and soil nitrogen content were the primary biotic and abiotic factors regulating microbial-derived and plant-derived C in both cropland and VR. However, soil phosphorus content was the main factor in cropland, while climatic factors such as mean annual precipitation were more important in VR. These results provided evidence that long-term natural revegetation enhanced SOC sequestration by greater contribution of plant-derived C to SOC formation compared to cropping. These findings underscore the synergistic contribution of vegetation and microorganisms to long-term SOC sequestration, offering insights into the different mechanisms of carbon formation during VR and cropping processes, and providing support for optimizing land management to achieve global carbon neutrality goals.

Mitochondrial dynamics and psychiatric disorders: The missing link.

Elucidating the molecular mechanisms of psychopathology is crucial for optimized diagnosis and treatment. Accumulating literature has underlined how mitochondrial bioenergetics affect major psychiatric disorders. However, how mitochondrial dynamics, a term addressing mitochondria quality control, including mitochondrial fission, fusion, biogenesis and mitophagy, is implicated in psychopathologies remains elusive. In this review we summarize the existing literature on mitochondrial dynamics perturbations in psychiatric disorders/neuropsychiatric phenotypes. We include preclinical/clinical literature on mitochondrial dynamics recalibrations in anxiety, depression, post-traumatic stress disorder (PTSD), bipolar disorder and schizophrenia. We discuss alterations in mitochondrial network, morphology and shape; molecular markers of the mitochondrial dynamics machinery and mitochondrial DNA copy number (mtDNAcn) in animal models and human cohorts in brain and peripheral material. By looking for common altered mitochondrial dynamics patterns across diagnoses/phenotypes, we highlight mitophagy and biogenesis as regulators of anxiety and depression pathophysiology, respectively, as well as the fusion mediator dynamin-like 120kDa protein (Opa1) as a molecular hub contributing to psychopathology. Finally, we comment on limitations and future directions in this novel neuropsychiatry field.

A Polarizable Forcefields for Glyoxal Acetals as Electrolyte Components for Lithium-Ion Batteries.

In this work we have derived the parameters of an AMOEBA-like polarizable forcefield for electrolytes based on tetramethoxy and tetraethoxy-glyoxal acetals, and propylene carbonate. The resulting forcefield has been validated using both ab-initio data and the experimental properties of the fluids. Using molecular dynamics simulations, we have investigated the structural features and the solvation properties of both the neat liquids and of the corresponding 1 M LiTFSI electrolytes at the molecular level. We present a detailed analysis of the Li ion solvation shells, of their structure and highlight the different behavior of the solvents in terms of their molecular structure and coordinating features.

When is lethal deceptive pollination maintained? A population dynamics approach.

BACKGROUND AND AIMS: Not all plant-pollinator interactions are mutualistic, and in fact, deceptive pollination systems are widespread in nature. The genus Arisaema has a pollination system known as lethal deceptive pollination, in which plants not only attract pollinating insects without providing any rewards, but also trap them until they die. Many Arisaema species are endangered from various disturbances including reduction in forest habitat, modification of the forest understory owing to increasing deer abundance, and plant theft for horticultural cultivation. We aimed to theoretically investigate how lethal deceptive pollination can be maintained from a demographic perspective and how plant and pollinator populations respond to different types of disturbance. METHODS: We developed and analysed a mathematical model to describe the population dynamics of a deceptive plant species and its victim pollinator. Calibrating the model based on empirical data, we assessed the conditions under which plants and pollinators could coexist, while manipulating relevant key parameters. KEY RESULTS: The model exhibited qualitatively distinct behaviours depending on certain parameters. The plant becomes extinct when it has a low capability for vegetative reproduction and slow transition from male to female, and plant-insect co-extinction occurs especially when the plant is highly attractive to male insects. Increasing deer abundance has both positive and negative effects because of removal of other competitive plants and diminishing pollinators, respectively. Theft for horticultural cultivation can readily threaten plants whether male or female plants are frequently collected. The impact of forest habitat reduction may be limited compared to that of other disturbance types. CONCLUSIONS: Our results have emphasised that the demographic vulnerability of lethal deceptive pollination systems would differ qualitatively from that of general mutualistic pollination systems. It is therefore important to consider the demographics of both victim pollinators and deceptive plants to estimate how endangered Arisaema populations respond to various disturbances.

Ultrafast and Coherent Dynamics in a Solvent Switchable "Pink Box" Perylene Diimide Dimer.

Perylene diimide (PDI) dimers and higher aggregates are key components in organic molecular photonics and photovoltaic devices, supporting singlet fission and symmetry breaking charge separation. Detailed understanding of their excited states is thus important. This has proven challenging because interchromophoric coupling is a strong function of dimer architecture. Recently, a macrocyclic PDI dimer was reported in which excitonic coupling could be turned on and off simply by changing the solvent. This presents a useful case where coupling is modified without synthetic changes to tune supramolecular structure. Here we present a detailed study of solvent dependent excited state dynamics in this dimer by means of coherent multidimensional spectroscopy. Spectral analysis resolves the different coupling strengths, which are consistent with solvent dependent changes in dimer conformation. The strongly coupled conformer forms an excimer within 300 fs. The low-frequency Raman active modes recovered from two-dimensional electronic spectra reveal frequencies characteristic of exciton coupling. These are assigned to modes modulating the coupling from the corresponding DFT calculations. Further analysis reveals a time dependent frequency during excimer formation. Analysis of two-dimensional "beatmaps" reveals features in the coupled dimer which are not predicted by the displaced harmonic oscillator model and are assigned to vibronic coupling.

The impact of fangxian huangjiu on the fermentation quality and microbial community dynamics of cigar wrapper leaves.

Introduction: Cigar wrapper leaves (CWLs) plays a crucial role in reflecting cigar overall quality. Originating from the Qinba region of China, Fangxian Huangjiu (FHJ) is distinctive from other varieties of Huangjiu. Methods: To investigate the effects of FHJ on enhancing the aroma and quality of CWLs, as well as the consequent alterations in microbial communities, Gas Chromatography-Mass Spectrometry (GC-MS) coupled with Odor Active Value (OAV) analysis was utilized to evaluate the volatile aroma components of CWLs. Results and Discussion: The results indicated that the total amount of aroma compounds in CWLs reached 3,086.88 ug/g, increasing of 270.50% and 166.31% compared to the unfermented and naturally fermented groups, respectively. Among them, ß-ionone and 4,7,9-megastigmatrien-3-one from the FHJ fermentation group significantly influenced the sensory characteristics of CWLs. Metagenomic results demonstrated that FHJ fermentation enriched the abundance of both shared and unique microbial species in CWLs, while also increased the diversity of differential microbial species. Addition of FHJ effectively altered the microbial community structure of CWLs from a dominance of Staphylococcus to a prevalence of Staphylococcus, Aspergillus, Pseudomonas, and Acinetobacter. The interactions among these diverse microorganisms collectively contribute to the enhancement of the intrinsic quality of CWLs. This paper provides a theoretical basis for improving the quality of CWLs by FHJ and exploring the changes of microbial community structure and interaction between CWLs and FHJ.

Synthesis and characterization of gold(I) thiolate derivatives and bimetallic complexes for HIV inhibition.

Introduction: The human immunodeficiency virus (HIV) remains a significant global health concern, with a reported high infection rate of 38.4 million cases globally; an estimated 2 million new infections and approximately 700,000 HIV/AIDS-related deaths were reported in 2021. Despite the advent of anti-retroviral therapy (ART), HIV/AIDS persists as a chronic disease. To combat this, several studies focus on developing inhibitors targeting various stages of the HIV infection cycle, including HIV-1 protease. This study aims to synthesize and characterize novel glyco diphenylphosphino metal complexes with potential HIV inhibitory properties. Method: A series of new gold(I) thiolate derivatives and three bimetallic complexes, incorporating amino phosphines and thiocarbohydrate as auxiliary ligands, were synthesized using procedures described by Jiang, et al. (2009) and Coetzee et al. (2007). Structural elucidation and purity assessment of the synthesized compounds (1-11) were conducted using micro-analysis, NMR, and infrared spectrometry. Results and Discussion: Using molecular modeling techniques, three of the metal complexes were identified as potential HIV protease inhibitors, exhibiting strong binding affinity interactions with binding pocket residues. These inhibitors demonstrated an ability to inhibit the flexibility of the flap regions of the HIV protease, similar to the known HIV protease inhibitor, darunavir. This study sheds light on the promising avenues for the development of novel therapeutic agents against HIV/AIDS.

Water determines the intramolecular dynamics of proteins. En example of bovine serum albumin.

In this work, the terahertz time-domain spectroscopy method analyzed solutions of bovine serum albumin (BSA) in two high concentrations (50 and 334 mg/mL) at three pH values (2.5, 6.5, 8.5) and the same solvents without protein, at 25°C. The spectra of dry BSA were also recorded. For the first time, a method for determining the complex dielectric permittivity of protein molecules in aqueous solutions, without the dielectric contribution of the aqueous phase, is proposed. It is shown that the dielectric permittivity of dissolved and dry BSA (lyophilized, in the native conformation) differ significantly in the terahertz frequency range. These differences are small near 70 cm-1, but they increase greatly with decreasing frequency. It was found that the dielectric losses of protein molecules in solution are close to the dielectric losses of the aqueous environment, which in this frequency range are determined by intermolecular relaxation processes of water. Since dielectric losses are directly related to molecular dynamics, this fact shows that the intramolecular dynamics of the protein completely adjusts to the intermolecular dynamics of the aqueous environment. It also indicates that the native conformation does not determine all the fundamental characteristics of a protein molecule, in particular, it does not determine the dynamics of the protein, which significantly depends on the water environment.

Evaluating the efficacy of the punch-out technique in systemic-to-pulmonary shunts: A computational fluid dynamics approach.

BACKGROUND: Systemic-to-pulmonary shunt is a palliative procedure used to decrease pulmonary blood flow in congenital heart diseases. Shunt stenosis or occlusion has been reported to be associated with mortality; therefore, the management of thrombotic complications remains a challenge for most congenital cardiovascular surgeons. Despite its importance, the optimal method for shunt anastomosis remains unclear. OBJECTIVE: The study investigates the clinical benefits of the punch-out technique over conventional methods in the anastomosis process of Systemic-to-pulmonary shunt, focusing on its potential to reduce shunt-related complications. METHODS: Anastomotic models were created by two different surgeons employing both traditional slit and innovative punch-out techniques. Computational tomography was performed to construct three-dimensional models for computational fluid dynamics (CFD) analysis. We assessed the flow pattern, helicity, magnitude of wall shear stress, and its gradient. RESULTS: The anastomotic flow area was larger in the model using the punch-out technique than in the slit model. In CFD simulation, we found that using the punch-out technique decreases the likelihood of establishing a high wall shear stress distribution around the anastomosis line in the model. CONCLUSION: The punch-out technique emerges as a promising method in SPS anastomosis, offering a reproducible and less skill-dependent alternative that potentially diminishes the risk of shunt occlusion, thereby enhancing patient outcomes.

Targeting Caspases 3/6 and Cathepsins L/B May Decrease Laminopathy-Induced Apoptosis in Alzheimer's Disease.

Background: Laminopathy is a pathological manifestation observed in Alzheimer's disease (AD), leading to neuronal apoptosis. Objective: Our objective was to assess inhibitors of enzymes involved in laminopathy. Methods: The mRNA expression of the cathepsins L and B, caspases 3 and 6, lamins b1 and b2, granzymes A and B, and lamins A and C were extracted and analyzed from GSE5281 and GSE28146 datasets. A total of 145 ligands were selected for molecular docking. Subsequently, 10 ns and 100 ns atomistic molecular dynamics (MD) and Martini 3 were performed with NAMD for two selected ligands (PubChem id: 608841 and ChEMBL id: 550872). Results: The mRNA expression level highlighted caspase 6 and lamin A/C upregulation in the hippocampus of the AD samples, in contrast to cathepsin B, lamin b2, and caspase 3. Moreover, there was a strong correlation between the expression level of cathepsin B, lamin A/C, and caspase 6 in the AD group. The MD results suggested molecule with ChEMBL id of 550872 had higher free binding energy, while in longer simulation the molecule with PubChem id of 608841 was suggested to be more stable in complex with the receptor. Conclusions: Our findings suggest that lamins A/C, cathepsins B/L, caspase 6, and lamin B2 are associated with laminopathy as potential factors contributing to apoptosis in AD. We propose that simultaneous inhibition of caspases 6 and cathepsins L may decrease the rate of apoptosis triggered by lamin degradation. Nevertheless, further studies are required to confirm these observations due to the lack of in vivo findings.

Riemannian geometry for efficient analysis of protein dynamics data.

An increasingly common viewpoint is that protein dynamics datasets reside in a nonlinear subspace of low conformational energy. Ideal data analysis tools should therefore account for such nonlinear geometry. The Riemannian geometry setting can be suitable for a variety of reasons. First, it comes with a rich mathematical structure to account for a wide range of geometries that can be modeled after an energy landscape. Second, many standard data analysis tools developed for data in Euclidean space can be generalized to Riemannian manifolds. In the context of protein dynamics, a conceptual challenge comes from the lack of guidelines for constructing a smooth Riemannian structure based on an energy landscape. In addition, computational feasibility in computing geodesics and related mappings poses a major challenge. This work considers these challenges. The first part of the paper develops a local approximation technique for computing geodesics and related mappings on Riemannian manifolds in a computationally feasible manner. The second part constructs a smooth manifold and a Riemannian structure that is based on an energy landscape for protein conformations. The resulting Riemannian geometry is tested on several data analysis tasks relevant for protein dynamics data. In particular, the geodesics with given start- and end-points approximately recover corresponding molecular dynamics trajectories for proteins that undergo relatively ordered transitions with medium-sized deformations. The Riemannian protein geometry also gives physically realistic summary statistics and retrieves the underlying dimension even for large-sized deformations within seconds on a laptop.

Resolving Atomic-Level Dynamics and Interactions of High-Molecular-Weight Hyaluronic Acid by Multidimensional Solid-State NMR.

High-molecular-weight (HMW) hyaluronic acid (HA) is a highly abundant natural polysaccharide and a fundamental component of the extracellular matrix (ECM). Its size and concentration regulate tissues' macro- and microenvironments, and its upregulation is a hallmark feature of certain tumors. Yet, the conformational dynamics of HMW-HA and how it engages with the components of the ECM microenvironment remain poorly understood at the molecular level. Probing the molecular structure and dynamics of HMW polysaccharides in a hydrated, physiological-like environment is crucial and also technically challenging. Here, we deploy advanced magic-angle spinning (MAS) solid-state NMR spectroscopy in combination with isotopic enrichment to enable an in-depth study of HMW-HA to address this challenge. This approach resolves multiple coexisting HA conformations and dynamics as a function of environmental conditions. By combining 13C-labeled HA with unlabeled ECM components, we detect by MAS NMR HA-specific changes in global and local conformational dynamics as a consequence of hydration and ECM interactions. These measurements reveal atom-specific variations in the dynamics and structure of the N-acetylglucosamine moiety of HA. We discuss possible implications for interactions that stabilize the structure of HMW-HA and facilitate its recognition by HA-binding proteins. The described methods apply similarly to the studies of the molecular structure and dynamics of HA in tumor contexts and in other biological tissues as well as HMW-HA hydrogels and nanoparticles used for biomedical and/or pharmaceutical applications.