Store-operated calcium release-activated calcium (CRAC) channels mediate a variety of cellular signaling functions. The CRAC channel pore-forming protein, Orai1, is a hexamer arranged with 3-fold symmetry. Despite its importance in moving Ca 2+ ions into cells, a detailed mechanistic understanding of Orai1 activation is lacking. Herein, a working model is proposed for the putative open state of Orai from Drosophila melanogaster (dOrai), which involves a ''twist-to-open'' gating mechanism. The proposed model is supported by energetic, structural, and experimental evidence. Fluorescent imaging demonstrates that each subunit on the intracellular side of the pore is inherently strongly cross-linked, which is important for coupling to STIM1, the pore activator, and graded activation of the Orai1 channel. The proposed model thus paves the way for understanding key aspects of calcium signaling at a molecular level.

Molecular self-assembly provides a chemical strategy for the synthesis of nanostructures by using the principles of nature, and peptides serve as the promising building blocks to construct adaptable molecular architectures. Recently, a series of heptapeptides with alternative hydrophobic and hydrophilic residues were reported to form amyloid-like structures, which are capable of catalyzing acyl ester hydrolysis with remarkable efficiency. However, information remains elusive about the atomic structures of the fibrils. What is the origin of the sequence-dependent catalytic activity? How is the ester hydrolysis catalyzed by the fibrils? In this work, the atomic structures of the aggregates were determined by using molecular modeling and further validated by solid-state NMR experiments, where the fibril with high activity adopts twisted parallel configuration within each layer, and the one with low activity is in flat antiparallel configuration. The polymorphism originates from the interactions between different regions of the building block peptides, where the delicate balance between rigidity and flexibility plays an important role. We further show that the p-nitrophenylacetate (pNPA) hydrolysis reactions catalyzed by two different fibrils follow a similar mechanism, and the difference in microenvironment at the active site between the natural enzyme and the present self-assembled fibrils should account for the discrepancy in catalytic activities. The present work provides understanding of the structure and function of self-assembled fibrils formed with short peptides at an atomic level and thus sheds new insight on designing aggregates with better functions.

The generalized energy-based fragmentation (GEBF) method is extended to allow calculations of nuclear magnetic resonance (NMR) chemical shifts of macromolecular and condensed-phase systems feasible at a low computational cost. In this approach, NMR shielding constants in a large system are evaluated as a linear combination of the corresponding quantities from a series of small "electrostatically embedded" subsystems. Comparison of NMR shielding constants from the GEBF-X method [where X is an electronic structure method, such as Hartree-Fock (HF), density functional theory (DFT), ...] with those from the conventional quantum chemistry method for two representative systems verifies that the GEBF approach can reproduce the results of the conventional quantum chemistry method very well. This procedure has further been applied to compute NMR shielding constants of a large foldamer and a supramolecular aggregate, and the N shielding constant for CHCN in the CHCl solvent. For the former two systems, the predicted H chemical shifts are in good agreement with the experimental data. For the CHCN/CHCl solution, the N shielding constant of CHCN is evaluated as the ensemble average of up to 200 sufficiently large CHCN/CHCl clusters from either classical or QM/MM (quantum mechanics/molecular mechanics) molecular dynamics (MD) simulations. Our results reveal that the gas-to-solution shift of N (from an isolated CHCN to the CHCN/CHCl solution) based on PM6-DH+/MM MD simulation is in good accord with the experimental value, outperforming those based on classical MD simulation and the previous polarizable continuum model using integral equation formalism (IEF-PCM) study. This study unravels that the generation of representative liquid structures is critical in evaluating the NMR shielding constants of condensed-phase systems.

Conformational transitions of protein between different states are often associated with their biological functions. These dynamic processes, however, are usually not easy to be well characterized by experimental measurements, mainly because of inadequate temporal and spatial resolution. Meantime, sampling of configuration space with molecular dynamics (MD) simulations is still a challenge. Here we proposed a robust two-ended data-driven accelerated (teDA2) conformational sampling method, which drives the structural change in an adaptively updated feature space without introducing a bias potential. teDA2 was applied to explore adenylate kinase (ADK), a model with well characterized “open” and “closed” states. A single conformational transition event of ADK could be achieved within only a few or tens of nanoseconds sampled with teDA2. By analyzing hundreds of transition events, we reproduced different mechanisms and the associated pathways for domain motion of ADK reported in the literature. The multiroute characteristic of ADK was confirmed by the fact that some metastable states identified with teDA2 resemble available crystal structures determined at different conditions. This feature was further validated with Markov state modeling with independent MD simulations. Therefore, our work provides strong evidence for the conformational plasticity of protein, which is mainly due to the inherent degree of flexibility. As a reliable and efficient enhanced sampling protocol, teDA2 could be used to study the dynamics between functional states of various biomolecular machines.

Projected Hartree–Fock theory provides an accurate description of many kinds of strong correlations but does not properly describe weakly correlated systems. On the other hand, single-reference methods, such as configuration interaction or coupled cluster theory, can handle weakly correlated problems but cannot properly account for strong correlations. Ideally, we would like to combine these techniques in a symmetry-projected coupled cluster approach, but this is far from straightforward. In this work, we provide an alternative formulation to identify the so-called disentangled cluster operators, which arise when we combine these two methodological strands. Our formulation shows promising results for model systems and small molecules.