JACS Au

Per- and polyfluoroalkyl substances (PFAS) are harmful environmental contaminants that bioaccumulate in human tissues and are linked to adverse health outcomes. While PFAS are known to bind to a variety of lipid binding proteins (LBPs), such as human serum albumin and fatty acid-binding proteins (FABPs), the broader molecular basis for their biological distribution and breadth of protein binding in humans remains unanswered. We hypothesize that some distribution and persistence of PFAS in humans arises from a distributed network of lipid transfer proteins that collectively solubilize and transport these compounds. To support this hypothesis, we investigated the interaction between various PFAS and human sterol carrier protein 2 (SCP2), a promiscuous, structurally distinct LBP with no previously reported binding with PFAS. Using a combination of screening, fluorescence displacement assays, protein structure prediction of PFAS-SCP2 complexes, and NMR experiments, we demonstrate for the first time that SCP2 is a PFAS-binding protein. Our findings establish SCP2 as a new PFAS-interacting protein, providing insights into the residues participating in these interactions and further supporting the hypothesis that PFAS engage with a broad network of LBPs to facilitate their distribution and persistence in the human body.

Heterochromatin protein 1 (HP1 is an intrinsic component of heterochromatin domains where it is involved in a diverse set of functions including heterochromatin spreading and organization, chromatin compaction and transcriptional silencing. It has been suggested that HP1 functions through a phase separation mechanism, a process that has been observed in vitro in the presence of N-terminal phosphorylation, nucleic acids and nucleosome arrays. HP1 can also interact with numerous binding partners that contain a specific motif called an HP1 access code (HAC). HACs recognize and bind to an interface formed by the chromoshadow (CSD) domains in the HP1 homodimer, the functional form of the protein. It has been shown that some HP1 binding partners can enhance its phase separation ability while others disrupt the process. Here, we focus on the interactions between HP1 and three binding partners, namely the p150 subunit of the chromatin assembly factor 1 (CAF-1), the N-terminal domain of the lamin B receptor (LBR), and the mitotic protein Shugoshin 1 (Sgo1). Using phase separation assays, we show that CAF-1 prevents HP1 phase separation while LBR and Sgo1 enhance it. Binding assays, mutational studies, NMR spectroscopy and computational analysis allow us to dissect the contributions of the HAC motifs, the charge patterns of the binding partner sequences and the role of N-terminal phosphorylation on HP1 in condensate formation. Our results demonstrate that each binding partner uniquely balances these contributions to modulate the properties of HP1, while electrostatic interactions dominate the regulation of phosphorylated HP1. These results suggest that HP1 binding partners play an important role in the modulation of its properties and the regulation of its functions in distinct biological contexts.

Parkinsons Disease (PD) is characterized by the aggregation of alpha-synuclein (aSyn), a presynaptic protein that transitions from a disordered monomer into beta-sheet rich amyloid fibrils. The precise triggers and mechanisms underlying aSyn misfolding and aggregation remain unclear, hindering the development of effective therapeutics. Monomeric aSyn is an intrinsically disordered protein (IDP) with high conformational flexibility. Local environmental factors, such as ion concentrations, can influence the conformational ensemble of aSyn, impacting its aggregation propensity and resulting in fibril polymorphism. In this study, we explore the impact of physiologically relevant ions, mainly Ca2+ and Na+, on the aggregation kinetics, monomer structural dynamics, and fibril polymorphism of aSyn. Using ThT fluorescence assays, we demonstrate that all ions accelerate aSyn aggregation, with Ca2+ having the most significant effect. Using Heteronuclear Single Quantum Correlation Nuclear Magnetic Resonance (1H-15NHSQC NMR) spectroscopy, we validate the specific binding of Ca2+ ions at the C-terminus, whereas Na+ ions display non-specific interactions along the sequence of aSyn. Small-angle neutron scattering (SANS) and hydrogen-deuterium exchange mass spectrometry (HDX-MS) further reveal that Na+ and Ca2+ induce distinct conformational changes in the aSyn monomer, with Na+ leading to more extended structures and Ca2+ promoting a moderate extension of the protein. Molecular dynamics simulations (MD) corroborate these findings, showing that Na+ ions increase the proteins extension, particularly between the non-amyloid beta component (NAC) region and the C-terminus, whereas Ca2+ ions bias the ensemble towards a more moderately elongated structure. Using MD, we further investigate the local environment and in particular the solvent effect and show the water persistence times in the hydration shell are also increased in the presence of Ca2+ ions, indicating that the aggregation propensity of the monomer is due to a combination of conformational bias of the monomer and solvent mobility. Atomic force microscopy (AFM) of aSyn fibrils formed under these different ionic conditions reveal distinct fibril polymorphs, suggesting that ion-induced conformational biases in the monomer contribute to the diversity of fibril structures. Collectively, these findings underscore the pivotal influence of the local ionic milieu in shaping the structure and aggregation propensity of aSyn, thus offering valuable insights into the molecular underpinnings of PD and potential therapeutic avenues aimed at manipulating aSyn conformational dynamics.

The rapid rise of antibiotic-resistant bacteria necessitates the search for alternative, unconventional solutions, such as targeting bacterial communication. Signal disruption can be achieved by enzymatic degradation of signaling compounds, reducing the expression of genes responsible for virulence, biofilm formation, and drug resistance while evading common resistance mechanisms. Therefore, enzymes with such activity have considerable potential as antimicrobial agents for medicine, industry, and other areas of life. Here, we designed molecular gates that control the binding site of penicillin G acylase to shift its preference from native substrate to signaling molecules. Using an ensemble-based design, three variants carrying triple-point mutations were proposed and experimentally characterized. Integrated inference from biochemical and computational analyses demonstrated that these three variants had markedly reduced activity towards penicillin and each preferred specific signal molecules of different pathogenic bacteria, exhibiting up to three orders of magnitude shifts in substrate specificity. Curiously, while we could consistently expand the pockets in these mutants, the reactive binding of larger substrates was limited, either by overpromoting or overstabilizing the pocket dynamics. Overall, we demonstrated the designability of this acylase for signal disruption and provided insights into the role of appropriately modulated pocket dynamics for such a function. The improved mutants, the knowledge gained, and the computational workflow developed to prioritize large datasets of promising variants may provide a suitable toolbox for future exploration and design of enzymes tailored to disrupt specific signaling pathways as viable antimicrobial agents.

As an intrinsically disordered protein, monomeric alpha synuclein (aSyn) constantly reconfigures and probes the conformational space. Long-range interactions across the protein maintain its solubility and mediate this dynamic flexibility, but also provide residual structure. Certain conformations lead to aggregation prone and non-aggregation prone intermediates, but identifying these within the dynamic ensemble of monomeric conformations is difficult. Herein, we used the biologically relevant calcium ion to investigate the conformation of monomeric aSyn in relation to its aggregation propensity. By using calcium to perturb the conformational ensemble, we observe differences in structure and intra-molecular dynamics between two aSyn C-terminal variants, D121A and pS129, and the aSyn familial disease mutants, A30P, E46K, H50Q, G51D, A53T and A53E, compared to wild-type (WT) aSyn. We observe that the more exposed the N-terminus and the beginning of the NAC region are, the more aggregation prone monomeric aSyn conformations become. N-terminus exposure occurs upon release of C-terminus interactions when calcium binds, but the level of exposure is specific to the aSyn mutation present. There was no correlation between single charge alterations, calcium affinity, or the number of ions bound on aSyns aggregation propensity, indicating that sequence or post-translation modification (PTM)-specific conformational differences between the N- and C-termini and the specific local environment mediate aggregation propensity instead. Understanding aggregation prone conformations of monomeric aSyn and the environmental conditions they form under will allow us to design new therapeutics targeted to the monomeric protein, to stabilise aSyn in non-aggregation prone conformations, by either preserving long-range interactions between the N- and C-termini or by protecting the N-terminus from exposure.

Protein stabilization is a "Holy Grail" of biocatalysis, and stability design is an area of intense research interest. While it is increasingly feasible to effectively increase enzyme thermostability, optimization without compromising activity or selectivity remains a significant challenge. Here, we use full-atom protein sequence design with sidechain conditioning (FAMPNN) to engineer thermostable variants of the borneol dehydrogenase from Salvia rosmarinus (SrBDH1), an enzyme from a family where unselective enzymes dominate, and selectivity is determined by dynamical considerations. By combining FAMPNN design with residue conservation analysis and avoiding active site residues, we were able to computationally design SrBDH1 variants with up to 10 {degrees}C enhanced thermostability and strongly increased half-life time at elevated temperature, while retaining selectivity towards (+)-borneol. This design framework, integrating de novo and physics-based protein design tools, demonstrates that stability can be enhanced without disrupting functionally relevant dynamics, providing a route to engineer robust and selective biocatalysts. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/719482v1_ufig1.gif" ALT="Figure 1"> View larger version (97K): org.highwire.dtl.DTLVardef@1a35073org.highwire.dtl.DTLVardef@f6c56dorg.highwire.dtl.DTLVardef@11b965forg.highwire.dtl.DTLVardef@2d6eef_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

NSD2 is a histone methyltransferase that modifies lysine 36 in histone H3 (H3K36), playing a central role in chromatin organization and transcriptional regulation. Oncogenic mutations, such as E1099K and T1150A in NSD2, have been associated with hyperactive methylation, but the molecular mechanisms underlying this gain of function remain poorly understood. In this study, we performed all-atom molecular dynamics simulations on models of NSD2 bound to the nucleosome for the wild type (WT), E1099K, T1150A, and the E1099K/T1150A double mutant. Analysis of MD simulations reveals that the global dynamics of the enzymes remain unaltered upon mutations. The time-lagged independent component analysis (tICA) and Markov state modeling uncovered fundamental differences in free-energy landscapes among the variants. The WT NSD2 exhibited energetically and kinetically unfavorable transitions between the macrostates along with extended enzyme-substrate distances. On the other hand, the mutant systems demonstrate reduced SAM-H3K36 distances with modified energy landscapes that facilitate transitions or favor prolonged occupancy of catalytically competent states. Importantly, the mutations reorganize the network of intramolecular contacts around the catalytic site, SAM-binding pocket, and histone-binding interface, optimizing substance engagement geometry. These findings demonstrate that oncogenic mutations achieve hyperactivity through strategic reorganization of conformational dynamics rather than simple destabilization, balancing local flexibility with global stability to enhance catalytic efficiency. Our results provide mechanistic insights into NSD2 dysregulation in cancer and establish a framework to develop allosteric inhibitors that target the enzymes dynamic landscape.

Protein phosphatase 2A containing the B56{delta} regulatory subunit (PP2A-B56{delta}) is a critical signaling enzyme whose dysregulation is associated with cancer, neurodegenerative disorders, and Jordan's syndrome, a severe intellectual disability disorder caused by mutations in B56{delta}. Unlike other PP2A holoenzymes, PP2A-B56{delta} is regulated through a unique dual autoinhibition mechanism in which the N- and C-arms occlude the catalytic site while a substrate-mimicking short linear motif (SLiM) blocks the substrate-binding pocket. Although disease-associated mutations have been shown to alter enzyme activity, the molecular mechanism underlying activation of PP2A-B56{delta} and the effects of pathogenic mutations remain poorly understood. Here, we combined cryo-electron microscopy (cryo-EM), enhanced-sampling molecular dynamics (MD) simulations, Markov state model (MSM) construction, and transition-state analysis using Transition State identification via Dispersion and vAriational principle Regularized neural networks (TS-DAR) to characterize the conformational landscape of the disease variant E198K. Our cryo-EM analysis identified two distinct structures of E198K: an inactive closed-form with the N/C-arms resolved and an active loose-form in which the N/C-arms become highly flexible and could not be fully resolved. These structures therefore established that activation is governed by conformational changes of the N/C-arms but did not reveal the underlying mechanism. Starting from the inactive closed-form, we generated over 1,600 trajectories with an average length of 1,260 ns combined for E198K and wild-type (WT) PP2A-B56{delta}. TS-DAR identified four metastable states and two major activation pathways connecting inactive and active conformations. We found that activation occurs through progressive loosening of the N/C-arm interface while maintaining the overall holoenzyme architecture, rather than a complete opening of the interface. This mechanism exposes both the catalytic site and substrate-binding pocket. Comparison of E198K and WT revealed that the disease-associated mutation shifts the conformational equilibrium toward active states while leaving the transition-state ensemble largely unchanged. Mechanistically, E198K disrupts a salt-bridge network and weakens interactions between the internal loop and the C-arm that normally stabilize active-site occlusion. The resulting increase in C-arm mobility promotes active-site exposure and explains the elevated catalytic activity of the mutant. Together, these findings establish a previously uncharacterized activation mechanism for PP2A-B56{delta} and provide an atomic-level explanation for how the pathogenic E198K mutation allosterically promotes holoenzyme activation.

CHI3L1 (YKL-40) is a chitinase-like glycoprotein involved in immune regulation, tissue remodeling, and cancer, yet the molecular principles governing its glycan interactions remain incompletely defined. Previous reports suggested that CHI3L1 can bind to chitin oligosaccharides (COS) and glycosaminoglycan (GAG) ligands, however, the molecular basis and binding sites underlying these interactions remain controversial. Here, a combination of biophysical and computational methods is employed to shed light on carbohydrate interactions of the protein and delineate a potential crosstalk between its glycan-binding interfaces. Our results demonstrate that COS and GAGs bind to distinct, non-overlapping sites on CHI3L1. Both ligand classes exhibit a strong dependence of binding affinity on the degree of polymerization. Molecular dynamics simulations, supported by mutational analysis, identify a GAG-binding site centered on residues R144, R145, and K147 and reveal an additional distal interaction site for longer GAG ligands. Biophysical and biochemical assays fail to confirm a previously proposed allo- or orthosteric interaction between both binding sites. However, physiologically relevant protein-protein interactions mediated by the chitin binding site of CHI3L1 are differentially regulated by GAG and COS ligands. COS inhibit binding of galectin-3 to CHI3L1, whereas GAG ligands enhance the affinity between the proteins by ca. 14-fold. Together, these findings establish CHI3L1 as a dual carbohydrate-binding protein with distinct recognition interfaces and reveal a previously unrecognized role for GAGs in modulating CHI3L1-mediated signaling interactions.

Proteins often harness extensive motions of domains and subunits to promote their function. Deciphering how these movements impact activity is key for understanding lifes molecular machinery. The enzyme adenylate kinase is an intriguing example for this relationship; it ensures efficient catalysis by large- scale domain motions that lead to the enclosure of the bound substrates ATP and AMP. At high concentrations, AMP also operates as an allosteric inhibitor of the protein. Surprisingly, the enzyme is activated by urea, a compound commonly acting as a denaturant. Combining single-molecule FRET spectroscopy and enzymatic activity studies, we find that urea interferes with two key mechanisms that contribute to enzyme efficacy. First, urea promotes the open conformation of the enzyme, aiding the proper positioning of the substrates. Second, urea decreases AMP affinity, paradoxically facilitating a more efficient progression towards the catalytically active complex. These results signify the important interplay between conformational dynamics and chemical steps, including binding, in the activity of enzymes. State-of-the-art tools, such as single-molecule fluorescence spectroscopy, offer new insights into how enzymes balance different conformations to regulate activity.

Many enzymes display non-Arrhenius behaviour with curved Arrhenius plots in the absence of denaturation. There has been significant debate about the origin of this behaviour and recently the role of the activation heat capacity [Formula] has been widely discussed. If enzyme-catalysed reactions occur with appreciable negative values of [Formula] (arising from narrowing of the conformational space along the reaction coordinate), then curved Arrhenius plots are a consequence. To investigate these phenomena in detail, we have collected high precision temperature-rate data over a wide temperature interval for a model glycosidase enzyme MalL, and a series of mutants that change the temperature-dependence of the enzyme-catalysed rate. We use these data to test a range of models including macromolecular rate theory (MMRT) and an equilibrium model. In addition, we have performed extensive molecular dynamics (MD) simulations to characterise the conformational landscape traversed by MalL in the enzyme-substrate complex and an enzyme-transition state complex. We have crystallised the enzyme in a transition state-like conformation in the absence of a ligand and determined an X-ray crystal structure at very high resolution (1.10 [A]). We show (using simulation) that this enzyme-transition state conformation has a more restricted conformational landscape than the wildtype enzyme. We coin the term "transition state-like conformation (TLC)" to apply to this state of the enzyme. Together, these results imply a cooperative conformational transition between an enzyme-substrate conformation (ES) and a transition-state-like conformation (TLC) that precedes the chemical step. We present a two-state model as an extension of MMRT (MMRT-2S) that describes the data along with a convenient approximation with linear temperature dependence of the activation heat capacity (MMRT-1L) that can be used where fewer data points are available. Our model rationalises disparate behaviour seen for MalL and a thermophilic alcohol dehydrogenase and is consistent with a raft of data for other enzymes. Our model can be used to characterise the conformational changes required for enzyme catalysis and provides insights into the role of cooperative conformational changes in transition state stabilisation that are accompanied by changes in heat capacity for the system along the reaction coordinate. TLCs are likely to be of wide importance in understanding the temperature dependence of enzyme activity, and other aspects of enzyme catalysis.

The FET family proteins, which includes FUS, EWS, and TAF15, are RNA chaperones instrumental in processes such as mRNA maturation, transcriptional regulation, and the DNA damage response. These proteins have clinical significance: chromosomal rearrangements in FET proteins are implicated in Ewing family tumors and related sarcomas. Furthermore, point mutations in FUS and TAF15 are associated with neurodegenerative conditions like amyotrophic lateral sclerosis and frontotemporal lobar dementia. The fusion protein EWS::FLI1, the causative mutation of Ewing sarcoma, arises from a genomic translocation that fuses the low-complexity domain (LCD) of EWS (EWSLCD) with the DNA binding domain of the ETS transcription factor FLI1. This fusion not only alters transcriptional programs but also hinders native EWS functions like splicing. However, the precise function of the intrinsically disordered EWSLCD is still a topic of active investigation. Due to its flexible nature, EWSLCD can form transient interactions with itself and other biomolecules, leading to the formation of biomolecular condensates through phase separation - a mechanism thought to be central to the oncogenicity of EWS::FLI1. In our study, we used paramagnetic relaxation enhancement NMR, analytical ultracentrifugation, light microscopy, and all-atom molecular dynamics (MD) simulations to better understand the self-association and phase separation tendencies of EWSLCD. Our aim was to elucidate the molecular events that underpin EWSLCD-mediated biomolecular condensation. Our NMR data suggest tyrosine residues primarily drive the interactions vital for EWSLCD phase separation. Moreover, a higher density and proximity of tyrosine residues amplify the likelihood of condensate formation. Atomistic MD simulations and hydrodynamic experiments revealed that the tyrosine-rich N and C-termini tend to populate compact conformations, establishing unique contact networks, that are connected by a predominantly extended, tyrosine-depleted, linker region. MD simulations provide critical input on the relationship between contacts formed within a single molecule (intramolecular) and inside the condensed phase (intermolecular), and changes in protein conformations upon condensation. These results offer deeper insights into the condensate-forming abilities of the FET proteins and highlights unique structural and functional nuances between EWS and its counterparts, FUS and TAF15.

Fumarate-adding enzymes (FAE) are a subset of the glycyl radical enzyme superfamily involved in anaerobic hydrocarbon degradation. Benzylsuccinate synthase (BSS) catalyzes the enantiospecific formation of R-benzylsuccinate from toluene and fumarate, initiating anaerobic toluene degradation. In this paper, we present a detailed theoretical study of the reaction mechanism using classical molecular dynamics and multiscale modelling (QM:MM). We describe the potential energy surface of the reaction, confirming the previously postulated mechanism. However, the multiscale character of our model allowed to elucidate the origins of several experimentally observed catalytic phenomena, such as the inversion of the configuration of the benzylic atom upon C-C bond formation, syn addition of the abstracted H atom back to the benzylsuccinyl radical, or kinetic isotope effects in the range of 1.7-2.1. The obtained model is supported by microkinetic analysis and was able to explain and quantitatively predict the strict R-enantioselectivity of BSS, which is not enforced by the binding orientation of the fumarate, but by dynamic kinetic behaviour of toluene in the active site leading to faster production of the R-enantiomer. We were also able to explain the experimentally observed slow H/D exchange in the product during incubation with BSS in D2O, confirming the partial reversibility of the reaction. Our study contributes to the elucidation of the catalytic processes catalyzed by BSS and its role in the bioremediation of hydrocarbon pollutants.

Enzyme engineering has produced numerous methods to optimize enzymes for biotechnological processes; however, less is known about how natural evolution creates new functionalities. We investigate the evolutionary emergence of enantioselectivity in plant borneol dehydrogenases (BDHs), which feature hydrophobic active-sites and are enantioselective towards dibornane-type monoterpenols. Ancestral sequence reconstruction provided a trajectory from the oldest unselective BDH ancestor N30 (E=12) toward the youngest selective ancestor N32, involving 19 mutations: 18 mutations are peripheral, one (I111L) occurs in the active-site. The mutation L111I in the hydrophobic pocket increased the selectivity of N30, while the back-mutation I111L decreased the selectivity of N32. Additional peripheral mutations (V136L/G169A/V183I) were required for high selectivity. Crystal structures suggested that protein dynamics, rather than structural changes shape these catalytic properties. Molecular simulations with funnel-metadynamics revealed a correlation between the active-sites solvent-accessible surface area (SASA) and selectivity. This potential evolutionary pathway shapes enantioselectivity, and guides future enzyme engineering campaigns.

The propensity for intrinsically disordered proteins to aggregate is heavily influenced by their surrounding environment. Here, we show that the mobility of the surrounding water molecules directly influences the aggregation rate of -synuclein (aSyn), a protein associated with Parkinsons disease. We observe that the addition of NaCl reduces the mobility of water, while addition of CsI increases the mobility of water. In turn, this reduces and increases the mobility of aSyn, respectively, given the change in strength and lifetime of the intermolecular forces. The reduction of aSyn mobility in the presence of NaCl ions leads to increased aggregation rates, which may be due to aggregation-competent conformations being stable for longer, thereby increasing the likelihood of establishing interactions between two adjacent monomers. In contrast, aSyn is more mobile when CsI is dissolved in the aqueous phase which leads to a reduction of successful monomeric interactions. We thus highlight the importance of the surrounding environment and describe how ion content can influence water mobility and the misfolding rate of amyloidogenic proteins, such as aSyn. By modulating the cellular environment to increase water mobility or finding small molecules to increase protein dynamics, new therapeutic targets may be found.

Fluorescent proteins (FP) are frequently used for studying proteins inside cells. In advanced fluorescence microscopy, FPs can report on additional intracellular variables. One variable is the local density near FPs, which can be useful in studying densities within cellular bio-condensates. Here, we show that a reduction in fluorescence lifetimes of common monomeric FPs reports increased levels of local densities. We demonstrate the use of this fluorescence-based variable to report the distribution of local densities within heterochromatin protein 1 (HP1) in mouse embryonic stem cells (ESCs), before and after early differentiation. We find that local densities within HP1 condensates in pluripotent ESCs are heterogeneous and cannot be explained by a single liquid phase. Early differentiation, however, induces a change towards a more homogeneous distribution of local densities, which can be explained as a liquid-like phase. In conclusion, we provide a fluorescence-based method to report increased local densities and apply it to distinguish between homogeneous and heterogeneous local densities within bio-condensates.

Renilla luciferase (RLuc) remains one of the most popular bioluminescence reporters, but its molecular principle has yet to be fully understood. Here, we reveal a detailed kinetic mechanism of the RLuc catalytic cycle which uncovers multiple limiting factors: (i) an oxygen-induced irreversible inactivation, (ii) a low oxygen saturation, and (iii) rate-limiting induced-fit conformational dynamics coupled with the product release. Furthermore, we could determine the actual enzyme kcat value at all saturating substrates to be 22 s-1. This value is 5-fold higher than the previously reported apparent kcat values determined at physiological, non-saturating oxygen concentration. Our integrative analysis by transient kinetics, X-ray crystallography, and molecular dynamics linked the rate-limiting flexible enzyme opening to the dynamics of the loops surrounding the active site, which prompted targeted engineering of this limiting step by loop grafting. The resulting variant AncFT-L14 (AncFT7) showed a prolonged stable light emission thanks to the selectively improved induced-fit kinetics. Additional characterization of AncFT-L14 identified increased catalytic efficiency kcat/Km, product inhibition factor Kp/Km, and a glow-type signal characteristic. Our results provide mechanistic details of RLuc catalysis and will govern future enzyme engineering to design the next generations of bioluminescence-based tools.

Phosphorylation is a major regulator of biomolecular condensation, yet it remains unclear whether clustered phosphoserines can directly tune phase behavior via metal-ion coordination. Here, using solution NMR spectroscopy and human heterochromatin protein 1 (HP1) as a model system, we show that stepwise phosphorylation of its N-terminal serine cluster generates a dynamic metal-responsive module that engages Mg{superscript 2}, Ca{superscript 2}, and Mn{superscript 2}, whereas the unmodified protein shows little or no response. Metal coordination lowers the saturation concentration of phosphorylated HP1, reshapes the temperature-dependent stability of its condensates, and modulates the effects of peptide regulators in an ion-specific manner. Our data support a model in which weak, transient metal-mediated contacts enhance intermolecular connectivity between phosphorylated HP1 molecules, promoting reversible condensation alongside canonical electrostatic interactions. These findings establish clustered phosphoserines as sequence-encoded metal-responsive elements that couple post-translational modification to the material properties of biomolecular condensates.

The protein tyrosine phosphatases (PTPs) SHP-1 and SHP-2 play complex roles in a variety of signaling pathways, including those involved in cancers and other diseases, making them important drug targets. These two PTPs have superimposable active sites, but different biological functions in vivo, including opposing roles in cancer development. Unique to these PTPs is the presence of two tandem Src homology 2 (SH2) domains, which regulate access to the phosphate binding site in the catalytic domain, through an autoinhibition mechanism. Studies of the allosteric regulation and dynamics of these PTPs, as well as associated drug discovery efforts, typically focus on autoinhibition rather than the dynamics of a catalytic loop in the phosphatase domain, the WPD-loop, which is essential for PTPase activity. However, recent deep mutational scanning data has demonstrated that oncogenic mutations also regulate WPD-loop motion in SHP-2. We provide here a detailed computational study of WPD-loop dynamics and catalysis in wild-type and mutant full-length and truncated (catalytic domain only) SHP-1 and SHP-2, demonstrating that many oncogenic residues lie on the allosteric pathways regulating WPD-loop dynamics. Mutations at these positions alter WPD-loop dynamics, disrupting the active site and negatively impacting catalysis. Further, our simulations provide molecular insight into the link between the presence of the SH2 domains and loop motion in the catalytic domain, and, importantly, how it differs between the two PTPs. Taken together, our work showcases the impact of altered WPD-loop motion in oncogenic SHP-1 and SHP-2 variants, opening new strategies for selectively targeting these important therapeutic enzymes.

Lanthipeptides are ribosomally synthesized and post-translationally modified peptides that are generated from precursor peptides through a dehydration and cyclization process in the biosynthetic pathways. In contrast to most other lanthipeptide synthetases, ProcM, a class II lanthipeptide synthetase, demonstrates high substrate tolerance. It is enigmatic that a single enzyme can catalyze the cyclization process of a diverse range of substrates with high fidelity. Previous studies suggested that the site-selectivity of lanthionine formation is determined by substrate sequence rather than by the enzyme. However, exactly how substrate sequence contributes to site-selective lanthipeptide biosynthesis is not clear. In this study, we performed molecular dynamic simulations for ProcA3.3 core peptide variants to explore how the predicted solution structure of the substrate without enzyme correlates to final product formation. Our simulation results support a model in which the secondary structure of the core peptide controls the ring pattern of the final product. We also demonstrate that the dehydration step in the biosynthesis pathway does not influence the site-selectivity of ring formation. In addition, we performed simulation for the core peptides of ProcA1.1 and 2.8, which are well-suited candidates to investigate the connection between order of ring formation and solution structure. Simulation results indicate that in both cases, C-terminal ring formation is more likely which was supported by experimental results. Our findings indicate that the substrate sequence and its solution structure can be used to predict the site-selectivity and order of ring formation, and that secondary structure is a crucial factor influencing the site-selectivity. Taken together, these findings will facilitate our understanding of the lanthipeptide biosynthetic mechanism and accelerate bioengineering efforts for lanthipeptide-derived products.