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Recent Submissions
Revised Data for "LignAmb25: A Comprehensive AMBER Force Field Addressing Lignin’s Structural and Chemical Diversity"
(2026) Lapsien, Marco; Bonus, Michele; Greb, Julian; Gohlke, Holger
LignAmb25 is a comprehensive force field for lignin molecular dynamics simulations implemented natively within the AMBER package. The force field includes parameters for all common monolignol units (p-coumaryl, coniferyl, caffeyl, and sinapyl alcohol) and their associated linkages (β O4, β 5, β β, β 1, 5 5, 5 O4, α-O4, BDO, and DBDO), along with less commonly encountered units such as tricin, spirodienones, and hydroxystilbenes. This enables simulations of both softwood and hardwood lignin structures with compositions that would be difficult to isolate experimentally. Force field parameters were initially derived from the GAFF2 force field and systematically optimized using quantum mechanical calculations at the ωB97X D4/def2 TZVPP level of theory on conformer ensembles derived via the CREST/CENSO conformational sampling toolchain. Partial atomic charges were derived using the RESP methodology, consistent with AMBER conventions. Experimentally measured crystal structures of lignin simulated with LignAmb25 accurately retain their packing based on calculations of the RMSD and density error compared to the deposited crystal structure, thereby exceeding the performance of the lignin force field for CHARMM. Additionally, LignAmb25 is shown to reliably estimate the enthalpy of vaporization and the absolute hydration free energy of lignin-related compounds. The LignAmb25 force field is provided in two variants: LignAmb25Solo, a standalone version not meant for use with other biomolecular force fields that focuses on accurate modelling of lignin solvent interactions, and LignAmb25HF, a version that is compatible with all other major biomolecular force fields in the AMBER molecular dynamics suite. This includes force fields of the GLYCAM (carbohydrates), ff19SB (proteins), and LIPID (lipids) families, as well as the DNA and RNA force fields routinely used in AMBER. The LignAmb25 force field will be distributed as of AMBER 26.
Intermediate stages in the origin of metabolism at a phosphorylating hydrothermal vent
(ScienceAdvances, 2026) Mrnjavac, Natalia; Hoffmann, Nadja K.; Schlikker, Manon L.; Burmeister, Maximilian; Schwander, Loraine; García García, Carolina; Brabender, Max; Steel, Mike; Huson, Daniel H.; Metzger, Sabine; Dherbassy, Quentin; Schink, Bernhard; Basen, Mirko; Moran, Joseph; Tüysüz, Harun; Preiner, Martina; Martin, William F.
The origin of life required the emergence of metabolism, an autocatalytic network of enzymatic reactions that synthesize amino acids, nucleotides and cofactors. At the origin of metabolism there were no enzymes—how did it start? Empirical studies addressing early metabolic evolution are lacking. Harnessing protein structures for metabolic enzymes, we identify intermediate states in primordial metabolic assembly. We show that enzymatic metabolism in the universal common ancestor was incomplete, undergoing final assembly independently in the lineages leading to Bacteria and Archaea. Native transition metals—Fe0, Co0, Ni0, Pd0—served as the catalytic forerunners of both enzymes and cofactors at metabolic origin while phosphite supplied energy, as it phosphorylates AMP to ADP and serine to phosphoserine using native metal catalysts in water. Phosphite and native metals occur in serpentinizing hydrothermal systems, identifying an energy-supplying, catalytic site of metabolic origin. Cofactors liberated nascent metabolism from native metal catalysts, engendering its autocatalytic state.
Cellular and subcellular heterogeneity of astrocytic Na⁺ homeostasis tuning astrocytes into functionally distinct subgroups in mouse forebrain
(Springer, 2026-05-31) Jan Meyer; Viola Bornemann; Alok Bhattarai; Sara Eitelmann; Petr Unichenko; Simone Durry; Karl W. Kafitz; Nicholas Chalmers; Jianfeng Fan; Ruth Beckervordersandforth; Christian Henneberger; Ghanim Ullah; Christine R. Rose
Overcoming bottlenecks for microbial production of the low-caloric sweetener D-allulose from D-glucose by evolutionary engineering
(2026) Gentile, Rocco; Gohlke, Holger
The low-calorie sugar D-allulose is a promising alternative to D-sucrose and high-fructose corn syrup, but its microbial production from D-glucose at mesophilic temperatures is limited by insufficient D-glucose isomerase (XylA) activity. Here, we overcome this bottleneck by evolving a Corynebacterium glutamicum selection strain whose growth strictly depends on XylA function. This strategy yielded a XylA variant with a nine-fold higher catalytic efficiency, sugar transporter variants (IolT1) with ten-fold increased activity for D-glucose and D-fructose, and hints for co-transport of these sugars by the D-sucrose transporter PtsS. Molecular dynamics simulations provided mechanistic explanations for the adaptive mutations. Combining the evolved enzymes with a suitable D-allulose 3-epimerase in a highly engineered chassis strain enabled whole-cell conversion of D-glucose to D-allulose with a 15% yield at 30 °C. This performance rivals high-temperature immobilized enzyme processes while avoiding enzyme purification and immobilization, offering an alternative for low-calorie sweetener production.
Data for "LignAmb25: A Comprehensive AMBER Force Field Addressing Lignin’s Structural and Chemical Diversity"
(2026) Lapsien, Marco; Bonus, Michele; Greb, Julian; Gohlke, Holger
LignAmb25 is a comprehensive force field for lignin molecular dynamics simulations implemented natively within the AMBER package. The force field includes parameters for all common monolignol units (p-coumaryl, coniferyl, caffeyl, and sinapyl alcohol) and their associated linkages (β O4, β 5, β β, β 1, 5 5, 5 O4, α-O4, BDO, and DBDO), along with less commonly encountered units such as tricin, spirodienones, and hydroxystilbenes. This enables simulations of both softwood and hardwood lignin structures with compositions that would be difficult to isolate experimentally. Force field parameters were initially derived from the GAFF2 force field and systematically optimized using quantum mechanical calculations at the ωB97X D4/def2 TZVPP level of theory on conformer ensembles derived via the CREST/CENSO conformational sampling toolchain. Partial atomic charges were derived using the RESP methodology, consistent with AMBER conventions. Experimentally measured crystal structures of lignin simulated with LignAmb25 accurately retain their packing based on calculations of the RMSD and density error compared to the deposited crystal structure, thereby exceeding the performance of the lignin force field for CHARMM. Additionally, LignAmb25 is shown to reliably estimate the enthalpy of vaporization and the absolute hydration free energy of lignin-related compounds. The LignAmb25 force field is provided in two variants: LignAmb25Solo, a standalone version not meant for use with other biomolecular force fields that focuses on accurate modelling of lignin solvent interactions, and LignAmb25HF, a version that is compatible with all other major biomolecular force fields in the AMBER molecular dynamics suite. This includes force fields of the GLYCAM (carbohydrates), ff19SB (proteins), and LIPID (lipids) families, as well as the DNA and RNA force fields routinely used in AMBER. The LignAmb25 force field will be distributed as of AMBER 26.
Heterogeneity of astrocyte density, morphology and connexins in the mouse hippocampus
(2025-12-19) Uelwer, Annika; Sivakumar, Mamitha; Umirdinov, Khojimurod; Purath, Fathima Faiba A.; Oluma, Lensa; Anstötz, Max; von Gall, Charlotte; Ali, Amira A. H.
The hippocampal formation is crucial for episodic learning and memory. In addition to neurons, astrocytes have also received increasing attention in recent years as essential components of brain networks by regulating the blood-brain barrier, eliminating waste products via the glymphatic system, supporting neuronal activity by providing energy supply and metabolic substrates, and regulating extracellular neurotransmitter levels. Astrocytes are heterogeneous and highly dynamic cells that respond to neuronal activity and dysfunction via morphological and functional changes. Astrocytic connexins (Cx) 30 and 43 form the molecular basis for gap junctions and hemichannels and are, thus, central to the coupling, intercellular communication and network integration of astrocytes in the brain. However, little is known about the spatial heterogeneity of astrocyte density, morphology and Cx expression in the subregions and layers of the hippocampus.
Therefore, in this study, we used immunohistochemistry to analyze the density and detailed morphological features of astrocytes and the spatial distribution of Cx30 and Cx43 in the layers of CA1, CA3 and dentate gyrus (DG). Astrocyte density correlated positively with the intensity of Cx30- and Cx43-immunoreaction (Ir). The stratum lacunosum moleculare (SLM) of CA1 and CA3 and the subgranular zone (SGZ) of DG showed the highest density of GFAP-positive (+) astrocytes and the strongest Cx30- and Cx43-Ir. The GFAP+ astrocytic processes had the largest radial extent in the pyramidal layer of CA1 and CA3 and in the granular layer of the DG.
Our study provides a comprehensive anatomical and comparative mapping of astrocytic density, morphology and Cx distribution in the mouse hippocampus and provides an important basis for further studies on the dynamics of neuron-glial interaction under different physiological and pathological conditions.