Biology subjects

Andersen, J. L.

Publications and source records attributed to Andersen, J. L..

10 recordsLinked to original sources

bioRxiv2025

Computational Approaches in Chemical Space Exploration for Carbon Fixation Pathways

Chemical space exploration is an important part of chemistry and biology, enabling the discovery and optimization of metabolic pathways, advancing synthetic metabolic functions, and understanding biochemical network evolution. We use a graph-based computational approach implemented in the cheminformatics software MOD, integrated with Integer Linear Programming (ILP) optimization, to systematically search chemical spaces. This approach allows for flexible and targeted queries, including identification of autocatalytic cycles, thermodynamic considerations, and discovery of novel enzymatic cascades. Specifically, we explore the chemical space of natural and artificial carbon fixation pathways defined from relevant enzyme reactions. By applying different optimization criteria, we identify new varieties and recombinations of natural autocatalytic pathways, and compare the properties of the pathways. This work highlights the versatility of graph-based cheminformatics for the purpose of chemical space exploration and artificial pathway design. Potential applications of this framework extend to carbon capture technologies, improved agricultural yields, and value-added chemical production, advancing efforts to address global sustainability challenges.

systems biology↗

bioRxiv2025

Characterization of the BRAF interactome identifies BRAFV600E<=>TP53 interaction in melanoma

Melanoma is a highly aggressive and frequently metastatic cancer with its incidence reported to be on the rise. Although most oncogenic drivers in melanoma converge on activation of the RAS>RAF>MEK>ERK MAPK signaling pathway, not all MAPK-activating mutations are recurrently observed in this disease, suggesting a unique functional role for BRAFV600E, which is present in [~]50% of all melanoma cases. However, the prevalence of BRAFV600E alterations over other known MAPK-promoting oncoproteins raises questions regarding whether BRAFV600E possesses additional functions outside of MAPK pathway activation. Thus, we performed TurboID to differentiate the interactome between wild-type BRAF and BRAFV600E. We identified novel interacting partners of normal vs. BRAFV600E, most strikingly being the tumor suppressor TP53. While TP53 is commonly altered or lost across many malignancies, it is notable that TP53 alterations are rare in melanoma. Our studies suggest that BRAFV600E can interact with and inactivate TP53, thus providing potential mechanistic explanation as to why TP53 inactivation or loss is infrequent in BRAFV600E-driven melanoma.

cancer biology↗

bioRxiv2025

Heavy Resistance Exercise Training in Older Men: A Responder and Inter-individual Variability Analysis

BackgroundHeavy resistance exercise training (HReT) effectively increases muscle mass and strength in groups of older individuals. However, the extent of inter-individual variability in response to HReT, and the possible existence of non-responders, remains unclear. The primary aim was to determine the presence of inter-individual variability in the response to prolonged HReT in healthy older individuals. Secondary aims were to classify individual responsiveness using a combination of gold-standard assessment methods, and to explore training progression and baseline levels as possible response moderators. MethodsWe conducted a secondary analysis of an 8- and 16-week intervention of thrice weekly HReT (EX) or continuation of a sedentary lifestyle (SED). 58 healthy men (age 72{+/-}5) were randomized into EX (n=38) or SED (n=20). Assessments were conducted at baseline, mid-intervention (8wk), and post-intervention (16wk) for five outcomes: Maximal voluntary contraction strength (MVC), rate of force development (RFD), quadriceps cross-sectional area (qCSA), and type I and II myofibre cross-sectional area (fCSA). Training compliance and progression (as measured by 1-repetition maximum (1RM)) were monitored. Inter-individual variability was assessed using the standard deviation of individual responses (SDIR). Individual change scores relative to a Typical Error (TE) were used to classify individuals as Poor, Trivial, Robust or Excellent responders. ResultsAt the group level, EX increased MVC, RFD, qCSA and type II fCSA by 19{+/-}14 %, 58{+/-}80 %, 3{+/-}4 % and 14{+/-}25 %, respectively, with no changes in SED. Inter-individual variability was observed for all outcomes. Individual responses to HReT were outcome- and time-dependent, with 31 participants (82%) being classified as Robust or Excellent responders, and two participants (5%) being Poor responders, following 16wk of HReT. Training compliance and 1RM progression did not account for the observed response variability following HReT. Lower baseline levels were associated with greater improvements; however, this did not account for the observed inter-individual variability. ConclusionsThis study provides strong evidence of inter-individual variability in response to HReT among healthy older men. Given the rarity of true non-responders, HReT should remain the universally recommended first-line strategy for enhancing muscle mass and strength in this population.

physiology↗

bioRxiv2023

Rules, hypergraphs, and probabilities: the three-level analysis of chemical reaction systems and other stochastic stoichiometric population processes

We consider problems in the functional analysis and evolution of combinatorial chemical reaction networks as rule-based, or three-level systems. The first level consists of rules, realized here as graph-grammar representations of reaction mechanisms. The second level consists of stoichiometric networks of molecules and reactions, modeled as hypergraphs. At the third level is the stochastic population process on molecule counts, solved for dynamics of population trajectories or probability distributions. Earlier levels in the hierarchy generate later levels combinatorially, and as a result constraints imposed in earlier and smaller layers can propagate to impose order in the architecture or dynamics in later and larger layers. We develop general methods to study rule algebras, emphasizing system consequences of symmetry; decomposition methods of flows on hypergraphs including the stoichiometric counterpart to Kirchhoffs current decomposition and work/dissipation relations studied in [1]; and the large-deviation theory for currents in a stoichiometric stochastic population process, deriving additive decompositions of the large-deviation function that relate a certain Kirchhoff flow decomposition to the extended Pythagorean theorem from information geometry. The latter result allows us to assign a natural probabilistic cost to topological changes in a reaction network of the kind produced by selection for catalyst-substrate specificity. We develop as an example a model of biological sugar-phosphate chemistry from a rule system published in [2]. It is one of the most potentially combinatorial reaction systems used by biochemistry, yet one in which two ancient, widespread and nearly unique pathways have evolved in the Calvin-Benson cycle and the Pentose Phosphate pathway, which are additionally nearly reverses of one another. We propose a probabilistic accounting in which physiological costs can be traded off against the fitness advantages that select them, and which suggests criteria under which these pathways may be optimal.

biochemistry↗

bioRxiv2023

The formation of ubiquitin rich condensates triggers recruitment of the ATG9A lipid transfer complex to initiate basal autophagy

Autophagy is an essential cellular recycling process that maintains protein and organelle homeostasis. ATG9A vesicle recruitment is a critical early step in autophagy to initiate autophagosome biogenesis. The mechanisms of ATG9A vesicle recruitment are best understood in the context of starvation-induced non-selective autophagy, whereas less is known about the signals driving ATG9A vesicle recruitment to autophagy initiation sites in the absence of nutrient stress. Here we demonstrate that loss of ATG9A or the lipid transfer protein ATG2 leads to the accumulation of phosphorylated p62 aggregates in the context of basal autophagy. Furthermore, we show that p62 degradation requires the lipid scramblase activity of ATG9A. Lastly, we present evidence that poly-ubiquitin is an essential signal that recruits ATG9A and mediates autophagy foci assembly in nutrient replete cells. Together, our data support a ubiquitin-driven model of ATG9A recruitment and autophagosome formation during basal autophagy.

cell biology↗

bioRxiv2023

Marked irregular myofiber shape is a hallmark of human skeletal muscle aging and is reversed by heavy resistance training

BackgroundAge-related loss of strength is disproportionally greater than the loss of mass, suggesting maladaptations in the neuro-myo-tendinous system. Myofibers are often misshaped in aged and diseased muscle, but systematic analyses of large sample sets are lacking. Our aim was to investigate myofiber shape in relation to age, exercise, myofiber type, species, and sex. MethodsPreviously collected vastus lateralis muscle biopsies (n=265) from 197 males and females, covering an age-span of 20 to 97 years, were examined. The gastrocnemius and soleus muscles of 7 C57BL/6 mice were also examined. Immunofluorescence and ATPase stainings of muscle cross-sections were used to measure myofiber cross-sectional area (CSA) and perimeter, from which a shape factor index (SFI) was calculated in a fiber type specific manner (type I and II in humans; type I, IIa, IIx and IIb in mice). Heavy resistance training (RT) was performed 3 times per week for 3-4 months by a subgroup (n=59). Correlation analyses were performed comparing SFI and CSA with age, muscle mass, maximal voluntary contraction (MVC), rate of force development (RFD), and specific force (MVC/muscle mass). ResultsIn human muscle, SFI was positively correlated with age for both type I (R2=0.20) and type II (R2=0.38) myofibers. When subjects were separated into age cohorts, SFI was lower for type I (p<0.001) and II (p<0.001) myofibers in Young (20-36) compared to Old (60-80), and higher for type I (p<0.05) and II (p<0.001) myofibers in the Oldest Old (>80) compared to Old. The increased SFI in old muscle was observed in myofibers of all sizes. Within all three age cohorts, type II myofibers SFI was higher than for type I myofibers (p<0.001), which was also the case in mice muscles (p<0.001). Across age cohorts, there was no difference between males and females in SFI for either type I (p=0.496/0.734) or II (p=0.176/0.585) myofibers. Multiple linear regression revealed that SFI, after adjusting for age and myofiber CSA, has independent explanatory power for 8 out of 10 indices of muscle mass and function. RT reduced SFI of type II myofibers in both Young and Old (p<0.001). ConclusionsHere, we identify type I and II myofiber shape in humans and mice as a hallmark of muscle ageing, that independently predicts volumetric and functional assessments of muscle health. RT reverts the shape of type II myofibers, indicating that lack of neuromuscular activation might lead to myofiber deformity.

physiology↗

bioRxiv2022

Preponderant Myosin Super-Relaxed State In Skeletal Muscle From Endurance Athletes

It has recently been established that myosin, the molecular motor protein, is able to exist in two conformations in relaxed skeletal muscle. These conformations are known as super-relaxed (SRX) and disordered-relaxed (DRX) states and are finely balanced to optimize skeletal muscle metabo-lism. Indeed, SRX myosins are thought to have a 10-fold reduction in ATP turnover compared to DRX myosins. Here, we investigated whether chronic physical activity in humans would be associated with changes in the proportions of SRX and DRX skeletal myosins. For that, we isolated mus-cle fibres from various athletic and sedentary populations and ran a loaded Mant-ATP chase proto-col. We observed that, in endurance-trained athletes, the amounts of myosin molecules in the SRX state was significantly greater than in age-matched sedentary individuals or than in strength athletes. To further assess whether this change would have an impact on the potency of a SRX-inducing pharmacological compound, Mavacamten, we performed similar analyses as above with and without the drug in muscle fibres from endurance athletes. Surprisingly, we found that 0.3 M of Mava-camten had only marginal effects. Altogether, our results indicate that chronic endurance training-status influences resting skeletal myosin conformations, and Mavacamten potency. Our findings also emphasize that environmental stimuli such as exercise can re-wire the molecular metabolism of human skeletal muscle through myosin. SummaryLewis et al., investigate how training-status influences myosin conformations involved in the resting metabolism of skeletal muscle. They find that, in endurance-trained athletes, skeletal myosin preferentially adopts an energy-saving conformation known as super-relaxed state, lowering the metabolic rate and affecting the potency of a super-relaxed state-inducing drug, Mavacamten.

physiology↗

bioRxiv2022

Activation and inhibition of the C-terminal kinase domain of p90 ribosomal S6 kinases

The p90 ribosomal S6 kinases (RSKs) contain two distinct catalytic kinase domains, the N-terminal and C-terminal kinase domains (NTKD and CTKD, respectively). The activation of CTKD is regulated by phosphorylation by extracellular signal-regulated kinase (ERK1/2) and an autoinhibitory L helix. Through a mutational series in vitro of the RSK CTKDs, we found a complex mechanism lifting autoinhibition that led us to design constitutively active RSK CTKDs. These are based on a phosphomimetic mutation and a C-terminal truncation (e.g. RSK2 T577E D694*) where a high activity in absence of ERK phosphorylation is obtained. Using these constructs, we characterize IC50 values of ATP-competitive inhibitors and provide a setup for determining specificity constants (kinact/Ki) of covalent CTKD inhibitors.

biochemistry↗

bioRxiv2021

The beryllium fluoride form of the Na+,K+-ATPase and the intermediates of the functional cycle

The Na+,K+-ATPase generates electrochemical gradients of Na+ and K+ across the plasma membrane. Here, we describe a 4.0 [A] resolution crystal structure of the pig kidney Na+,K+-ATPase stabilized by beryllium fluoride (denoted E2-BeFx). The structure shows high resemblance to the E2P phosphoenzyme obtained by phosphorylation from inorganic phosphate (Pi) and stabilised by cardiotonic steroids, and reveals a Mg2+ bound near the ion binding site II. Anomalous Fourier analysis of the crystals soaked in Rb+ (K+ congener) followed by a low resolution rigid-body refinement (6.9-7.5 [A]) revealed pre-occlusion transitions leading to activation of the desphosphorylation reaction. Mg2+ location indicates a site of an initial K+ recognition and acceptance upon binding to the outward-open E2P state after Na+ release. Despite the overall structural resemblance to the Pi-induced E2P phosphoform, BeFx inhibited enzyme is able to bind both ADP/ATP and ions - features that relate E2-BeFx complex to an intermediate of the functional cycle of the Na+,K+-ATPase prior E2P.

biochemistry↗

bioRxiv2018

Structures of the heart specific SERCA2a Ca2+-ATPase

The isoform 2a of sarco/endoplasmic reticulum Ca2+-ATPase (SERCA2a) performs active reuptake of cytoplasmic Ca2+ and is a major regulator of cardiac muscle contractility. Dysfunction or dysregulation of SERCA2a is associated with heart failure, while restoring its function is considered as a therapeutic strategy to restore cardiac performance, but its structure was not yet determined. Based on native, active protein purified from pig ventricular muscle, we present the first crystal structures of SERCA2a that were determined in the CPA-stabilized and H+-occluded [H2-3]E2-AlF4 - (3.3 [A]) form, arranged as parallel dimers, and the Ca2+-occluded [Ca2]E1-ATP (4.0 [A]) form. We compare these new structures to similar forms of the skeletal muscle SERCA1a and address structural, functional and regulatory differences. We show that the isoform specific motifs of SERCA2a allow a distinct regulation by post-translational modifications and affect the dynamic behavior, which may explain specific properties and regulation.

biochemistry↗