How do antiporters exchange substrates across the cell membrane? An atomic-level description of the complete exchange cycle in NarK

Major facilitator superfamily (MFS) proteins operate via three different mechanisms: uniport, symport, and antiport. Despite extensive investigations, the molecular understanding of antiporters is less advanced than that of other transporters due to the complex coupling between two substrates and the lack of distinct structures. We employ extensive all-atom molecular dynamics simulations to dissect the complete substrate exchange cycle of the bacterial NO₃^-/NO₂^- antiporter, NarK. We show that paired basic residues in the binding site prevent the closure of unbound protein and ensure the exchange of two substrates. Conformational transition occurs only in the presence of substrate, which weakens the electrostatic repulsion and stabilizes the transporter. Furthermore, we propose a state-dependent substrate exchange model, in which the relative spacing between the paired basic residues determines whether NO₃^- and NO₂^- bind simultaneously or sequentially. Overall, this work presents a general working model for the antiport mechanism within the MFS.

TLmutation: Predicting the Effects of Mutations Using Transfer Learning

A reccurring challenge in bioinformatics is predicting the phenotypic consequence of amino acid variation in proteins. With the recent advancements in sequencing techniques, sufficient genomic data has become available to train models that predict the evolutionary statistical energies, but there is still inadequate experimental data to directly predict functional effects. One approach to overcome this data scarcity is to apply transfer learning and train more models with available data sets. In this study, we propose a set of transfer learning algorithms we call TLmutation, which implements a supervised transfer learning algorithm that transfers knowledge from survival data of a protein to a particular function of that protein. This is followed by an unsupervised transfer learning algorithm that extends the knowledge to a homologous protein. We explore the application of our algorithms in three cases. First, we test the supervised transfer on 17 previously published deep mutagenesis data sets to complete and refine missing data points. We further investigate these data sets to identify which mutations build better predictors of variant functions. In the second case, we apply the algorithm to predict higher-order mutations solely from single point mutagenesis data. Finally, we perform the unsupervised transfer learning algorithm to predict mutational effects of homologous proteins from experimental data sets. These algorithms are generalized to transfer knowledge between Markov random field models. We show the benefit of our transfer learning algorithms to utilize informative deep mutational data and provide new insights into protein variant functions. As these algorithms are generalized to transfer knowledge between Markov random field models, we expect these algorithms to be applicable to other disciplines.

FingerprintContacts: Predicting Alternative Conformations of Proteins from Coevolution

Proteins are dynamic molecules which perform diverse molecular functions by adopting different three-dimensional structures. Recent progress in residue-residue contacts prediction opens up new avenues for the de novo protein structure prediction from sequence information. However, it is still difficult to predict more than one conformation from residue-residue contacts alone. This is due to the inability to deconvolve the complex signals of residue-residue contacts, i.e., spatial contacts relevant for protein folding, conformational diversity, and ligand binding. Here, we introduce a machine learning based method, called FingerprintContacts, for extending the capabilities of residue-residue contacts. This algorithm leverages the features of residue-residue contacts, that is, (1) a single conformation outperforms the others in the structural prediction using all the top ranking residue-residue contacts as structural constraints and (2) conformation specific contacts rank lower and constitute a small fraction of residue-residue contacts. We demonstrate the capabilities of FingerprintContacts on eight ligand binding proteins with varying conformational motions. Furthermore, FingerprintContacts identifies small clusters of residue-residue contacts which are preferentially located in the dynamically fluctuating regions. With the rapid growth in protein sequence information, we expect FingerprintContacts to be a powerful first step in structural understanding of protein functional mechanisms.

Divalent cations promote TALE DNA-binding specificity

Recent advances in gene editing have been enabled by programmable nucleases such as transcription activator-like effector nucleases (TALENs) and CRISPR–Cas9. However, several open questions remain regarding the molecular machinery in these systems, including fundamental search and binding behavior as well as role of off-target binding and specificity. In order to achieve efficient and specific cleavage at target sites, a high degree of target site discrimination must be demonstrated for gene editing applications. In this work, we studied the binding affinity and specificity for a series of TALE proteins under a variety of solution conditions using in vitro fluorescence methods and molecular dynamics (MD) simulations. Remarkably, we identified that TALEs demonstrate high sequence specificity only upon addition of small amounts of certain divalent cations (Mg²⁺, Ca²⁺). However, under purely monovalent salt conditions (K⁺, Na⁺), TALEs bind to specific and non-specific DNA with nearly equal affinity. Divalent cations preferentially bind to DNA over monovalent cations, which attenuates non-specific interactions between TALEs and DNA and further stabilizes specific interactions. Overall, these results uncover new mechanistic insights into the binding action of TALEs and further provide potential avenues for engineering and application of TALE- or TALEN-based systems for genome editing and regulation.

Molecular Mechanism of Brassinosteroid Perception by the Plant Growth Receptor BRI1

Brassinosteroids (BRs) are essential phytohormones, which bind to the plant receptor, BRI1, to regulate various physiological processes. The molecular mechanism of the perception of BRs by the ectodomain of BRI1 remains not fully understood. It also remains elusive why a substantial difference in biological activity exists between the BRs. In this work, we study the binding mechanisms of the two most bioactive BRs, brassinolide (BLD) and castasterone (CAT), using molecular dynamics simulations. We report free-energy landscapes of the binding processes of both ligands, as well as detailed ligand binding pathways. Our results suggest that CAT has a lower binding affinity compared to BLD due to its inability to form hydrogen-bonding interactions with a tyrosine residue in the island domain of BRI1. We uncover a conserved nonproductive binding state for both BLD and CAT, which is more stable for CAT and may further contribute to the bioactivity difference. Finally, we validate past observations about the conformational restructuring and ordering of the island domain upon BLD binding. Overall, this study provides new insights into the fundamental mechanism of the perception of the two most bioactive BRs, which may create new avenues for genetic and agrochemical control of their signaling cascade.

High temperature-mediated rocksalt to wurtzite phase transformation in cadmium oxide nanosheets and its theoretical evidence

Herein, a high temperature-induced phase transformation (PT) in chemically grown CdO thin films is demonstrated, and its corresponding electronic origin further investigated by density functional theory. In particular, the cubic rocksalt to hexagonal wurtzite PT in the CdO thin film annealed at 900 °C was confirmed by X-ray diffraction (XRD), which was consistent with the high-resolution transmission electron microscopy (TEM) results. Moreover, atomic force microscopy and scanning electron microscopy clearly evidenced the morphological evolution via the formation of a nanosheet network in the wurtzite-phase CdO film. The high temperature treatment also led to a significant enhancement in the optical band gap from 2.2 to 3.2 eV, as manifested by UV-visible spectroscopy. The enhanced surface roughness of the nanosheet caused a deviation in the net dipole moment, which may break the polarizable bonds and help in reducing the average dielectric constant, resulting in a band gap opening for the transformed phase. Furthermore, X-ray absorption spectroscopy at the oxygen k-edge revealed a notable shift in the inflection point of the absorption edge, while the X-ray photoelectron spectroscopy (XPS) Cd 3d and O 1s spectra suggested a gradual reduction in the CdO2 phase with an increase in annealing temperature. In addition, different complementary techniques including Rutherford backscattering and Raman spectroscopy were exploited to understand the aforementioned PT and its structural correlation. Finally, molecular dynamics simulation together with density functional theory calculation suggested that the symmetry modification at the Brillouin zone boundary provides a succinct signature for the PT in the CdO thin film.

Molecular Basis of the Glucose Transport Mechanism in Plants

The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane (SWEET, Sugars Will Eventually Be Exported Transporter). However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in the OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as for the glucose transport mechanism. SWEETs undergo a structural transition to outward-facing (OF), occluded (OC), and inward-facing (IF) and strongly support an alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly the same for OF, OC, and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and acts as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass-like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.

Ion Gel Dynamic Templates for Large Modulation of Morphology and Charge Transport Properties of Solution-Coated Conjugated Polymer Thin Films

Dynamic surfaces play a critical role in templating highly ordered complex structures in living systems but are rarely employed for directing assembly of synthetic functional materials. We design ion gel templates with widely tunable dynamics ( T_g) to template solution-coated conjugated polymers. We hypothesize that the ion gel expedites polymer nucleation by reconfiguring its surface to facilitate cooperative multivalent interactions with the conjugated polymer, validated using both experimental and computational approaches. Varying ion gel dynamics enables large modulation of alignment, molecular orientation, and crystallinity in templated polymer thin films. At the optimal conditions, ion-gel-templated films exhibit 55 times higher dichroic ratio (grazing incidence X-ray diffraction) and 49% increase in the relative degree of crystallinity compared to those templated by the neat polymer matrix. As a result, the maximum hole mobilities increase by factors of 4 and 11 along the π-π stacking and the backbone directions. Intriguingly, we observe a synergistic effect between the gel matrix and the ionic liquid that produces markedly enhanced templating effect than either component alone. Molecular dynamics simulations suggest that complementary multivalent interactions facilitated by template reconfigurability underlie the observed synergy. We further demonstrate field-effect transistors both templated and gated by ion gels with average mobility exceeding 7 cm² V^-1 s^-1.

Dodine as a Kosmo-Chaotropic Agent

Denaturants such as the guanidinium cation unfold proteins at molar concentrations, which interferes with ultraviolet- and infrared-based spectroscopy measurements. Dodine denatures some proteins cooperatively at a thousand-fold lower concentration, allowing for spectroscopy measurements. Nonetheless, dodine's microscopic mechanism of interaction with proteins is not understood. We probe the effect of dodine on α-helices and tertiary structure by investigating the stability of the small helical protein B. Experiments show that dodine promotes formation of helical structure (a kosmotropic effect), while inducing the loss of tertiary structure (a chaotropic effect). Although dodine destabilizes native protein structure, it does not lower the thermal denaturation midpoint temperature of protein B. All-atom simulations reveal the cause for both observations: The denaturant action of dodine's guanidyl headgroup is counteracted by its aliphatic tail, which stabilizes amphipathic helices and associates with an expanded protein core. The Janus-like behavior of headgroup and tail make dodine a simultaneous stabilizer-destabilizer or "kosmo-chaotrope".

Structural architecture of a dimeric class C GPCR based on co-trafficking of sweet taste receptor subunits

Class C G protein-coupled receptors (GPCRs) are obligatory dimers that are particularly important for neuronal responses to endogenous and environmental stimuli. Ligand recognition through large extracellular domains leads to the reorganization of transmembrane regions to activate G protein signaling. Although structures of individual domains are known, the complete architecture of a class C GPCR and the mechanism of interdomain coupling during receptor activation are unclear. By screening a mutagenesis library of the human class C sweet taste receptor subunit T1R2, we enhanced surface expression and identified a dibasic intracellular retention motif that modulates surface expression and co-trafficking with its heterodimeric partner T1R3. Using a highly expressed T1R2 variant, dimerization sites along the entire subunit within all the structural domains were identified by a comprehensive mutational scan for co-trafficking with T1R3 in human cells. The data further reveal that the C terminus of the extracellular cysteine-rich domain needs to be properly folded for T1R3 dimerization and co-trafficking, but not for surface expression of T1R2 alone. These results guided the modeling of the T1R2-T1R3 dimer in living cells, which predicts a twisted arrangement of domains around the central axis, and a continuous folded structure between transmembrane domain loops and the cysteine-rich domains. These insights have implications for how conformational changes between domains are coupled within class C GPCRs.

Free Energy Landscape of the Complete Transport Cycle in a Key Bacterial Transporter

PepT_So is a proton-coupled bacterial symporter, from the major facilitator superfamily (MFS), which transports di-/tripeptide molecules. The recently obtained crystal structure of PepT_So provides an unprecedented opportunity to gain an understanding of functional insights of the substrate transport mechanism. Binding of the proton and peptide molecule induces conformational changes into occluded (OC) and outward-facing (OF) states, which we are able to characterize using molecular dynamics (MD) simulations. The structural knowledge of the OC and OF state is important to fully understand the major energy barrier associated with the transport cycle. In order to gain functional insight into the interstate dynamics, we performed extensive all atom MD simulations. The Markov state model was constructed to identify the free energy barriers between the states, and kinetic information on intermediate pathways was obtained using the transition pathway theory (TPT). TPT shows that the OF state is obtained by the movement of TM1 and TM7 at the extracellular side approximately 12-16 Å away from each other, and the inward movement of TM4 and TM10 at the intracellular halves to 3-4 Å characterizes the OC state. Helix distance distributions obtained from MD simulations were compared with experimental double electron-electron resonance spectroscopy and were found to be in excellent agreement with previous studies. We also predicted the optimal positions for placement of methane thiosulfonate spin label probes to capture the slowest protein dynamics. Our finding sheds light on the conformational cycle of this key membrane transporter and the functional relationships between the multiple intermediate states.