Conformational Dynamics in Proteins: Entangled Slow Fluctuations and Nonequilibrium Reaction Events.

Proteins exhibit conformational fluctuations and changes over various time scales, ranging from rapid picosecond-scale local atomic motions to slower microsecond-scale global conformational transformations. In the presence of these intricate fluctuations, chemical reactions occur and functions emerge. These conformational fluctuations of proteins are not merely stochastic random motions but possess distinct spatiotemporal characteristics. Moreover, chemical reactions do not always proceed along a single reaction coordinate in a quasi-equilibrium manner. Therefore, it is essential to understand spatiotemporal conformational fluctuations of proteins and the conformational change processes associated with reactions. In this Perspective, we shed light on the complex dynamics of proteins and their role in enzyme catalysis by presenting recent results regarding dynamic couplings and disorder in the conformational dynamics of proteins and rare but rapid enzymatic reaction events obtained from molecular dynamics simulations.

Hydroxide Ion Mechanism for Long-Range Proton Pumping in the Third Proton Transfer of Bacteriorhodopsin.

In bacteriorhodopsin, representative light-driven proton pump, five proton transfers yield vectorial active proton translocation, resulting in a proton gradient in microbes. Third proton transfer occurs from Asp96 to the Schiff base on the photocycle, which is expected to be a long-range proton transfer via the Grotthuss mechanism through internal water molecules. Here, large-scale quantum molecular dynamics simulations are performed for the third proton transfer, where all the atoms (∼50000 atoms) are treated quantum-mechanically. The simulations demonstrate that two reaction paths exist along the water wire, namely, via hydronium and via hydroxide ions. The free energy analysis confirms that the path via hydroxide ions is considerably favorable and consistent with the observed lifetime of the transient water wire. Therefore, the proposed hydroxide ion mechanism, as in the first proton transfer, is responsible for the third long-range proton transfer.

Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations.

The main protease (Mpro) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) catalyzes the cleavage of polyproteins for viral replication. Here, large-scale quantum molecular dynamics and metadynamics simulations for ligand-free Mpro were performed, where all the atoms were treated quantum-mechanically, focusing on elucidation of the controversial active-site protonation state. The simulations clarified that the interconverting multiple protonation states exist in unliganded Mpro, and the catalytically relevant ion-pair state is more stable than the neutral state, which is consistent with neutron crystallography. The results highlight the importance of the ion-pair state for repurposing or discovering antiviral drugs that target Mpro.

Quantum-Mechanical Molecular Dynamics Simulations on Secondary Proton Transfer in Bacteriorhodopsin Using Realistic Models.

Bacteriorhodopsin (BR) transports a proton from intracellular to extracellular (EC) sites through five proton transfers. The second proton transfer is the release of an excess proton stored in BR into the EC medium, and an atomistic understanding of this whole process has remained unexplored due to its ubiquitous environment. Here, fully quantum mechanical (QM) molecular dynamics (MD) and metadynamics (MTD) simulations for this process were performed at the divide-and-conquer density-functional tight-binding level using realistic models (∼50000 and ∼20000 atoms) based on the time-resolved photointermediate structures from an X-ray free electron laser. Regarding the proton storage process, the QM-MD/MTD simulations confirmed the Glu-shared mechanism, in which an excess proton is stored between Glu194 and Glu204, and clarified that the activation occurs by localizing the proton at Glu204 in the photocycle. Furthermore, the QM-MD/MTD simulations elucidated a release pathway from Glu204 through Ser193 to the EC water molecules and clarified that the proton release starts at ∼250 µs. In the ubiquitous proton diffusion in the EC medium, the transient proton receptors predicted experimentally were assigned to carboxylates in Glu9 and Glu74. Large-scale QM-MD/MTD simulations beyond the conventional sizes, which provided the above findings and confirmations, were possible by adopting our Dcdftbmd program.

Hydroxide Ion Carrier for Proton Pumps in Bacteriorhodopsin: Primary Proton Transfer.

Bacteriorhodopsin (BR) is a model protein for light-driven proton pumps, where the vectorial active proton transport results in light-energy conversion. To clarify the microscopic mechanism of primary proton transfer from retinal Schiff base (SB) to Asp85 in BR, herein, we performed quantum-mechanical metadynamics simulations with the isolated BR model (∼3750 atoms). The simulations showed a novel proton transfer mechanism, viz. the hydroxide ion mechanism, in which the deprotonation of specific internal water (Wat452) yields the protonation of Asp85 via Thr89, after which the resulting hydroxide ion accepts the remaining proton from retinal SB. Systematic investigations adopting four sequential snapshots obtained by the time-resolved serial femtosecond crystallography revealed that proton transfer took 2-5.25 µs on the photocycle. The presence of Wat401, which is the main difference between snapshots at 2 and 5.25 µs, is found to be essential in assisting the primary proton transfer. Furthermore, the hydroxide ion mechanism was confirmed by the minimum energy path for the primary proton transfer in BR obtained by the nudged elastic band calculations with the embedded BR model (10,119 atoms), in which BR was embedded within lipid membranes in between water solvents.

Reversible Sodium Metal Electrodes: Is Fluorine an Essential Interphasial Component?

Alkaline metals are an ideal negative electrode for rechargeable batteries. Forming a fluorine-rich interphase by a fluorinated electrolyte is recognized as key to utilizing lithium metal electrodes, and the same strategy is being applied to sodium metal electrodes. However, their reversible plating/stripping reactions have yet to be achieved. Herein, we report a contrary concept of fluorine-free electrolytes for sodium metal batteries. A sodium tetraphenylborate/monoglyme electrolyte enables reversible sodium plating/stripping at an average Coulombic efficiency of 99.85 % over 300 cycles. Importantly, the interphase is composed mainly of carbon, oxygen, and sodium elements with a negligible presence of fluorine, but it has both high stability and extremely low resistance. This work suggests a new direction for stabilizing sodium metal electrodes via fluorine-free interphases.

Development of Large-Scale Excited-State Calculations Based on the Divide-and-Conquer Time-Dependent Density Functional Tight-Binding Method.

In this study, the divide-and-conquer (DC) method was extended to time-dependent density functional tight-binding (TDDFTB) theory to enable excited-state calculations of large systems and is denoted by DC-TDDFTB. The efficient diagonalization algorithms of TDDFTB and DC-TDDFTB methods were implemented into our in-house program. Test calculations of polyethylene aldehyde and p-coumaric acid, a pigment in photoactive yellow protein, in water demonstrate the high accuracy and efficiency of the developed DC-TDDFTB method. Furthermore, the (TD)DFTB metadynamics simulations of acridinium in the ground and excited states give reasonable p Ka values compared with the corresponding experimental values.

Sagittal splitting of the temporalis muscle for encephalo-myo-synangiosis to prevent ischemic complications due to a swollen temporalis muscle without inhibiting collateral developments in patients with moyamoya disease.

OBJECTIVEEncephalo-myo-synangiosis (EMS) is an effective revascularization procedure for the treatment of moyamoya disease (MMD). However, the temporalis muscle used for EMS sometimes swells and causes ischemic complications by compressing the underlying brain. This study aimed to elucidate the effect of sagittal splitting (SS) of the muscle for prevention of ischemic complications and its impact on the postoperative development of collateral vessels.METHODSIn this historical case-control study, we analyzed 60 hemispheres in adult patients with MMD who underwent EMS using the temporalis muscle from December 1998 to November 2017. The muscle was divided anteroposteriorly by coronal splitting, and the anterior, posterior, or both parts of the muscle were used for EMS in 17, 4, and 39 hemispheres, respectively. In cases performed after 2006, the muscle was halved by SS, and the medial half was used for EMS to reduce the muscle volume (n = 47). The degree of postoperative muscle swelling was evaluated by measuring the maximum thickness of the muscle on CT scans obtained 3 to 7 days after surgery. The collateral developments of the anterior deep temporal artery (aDTA), posterior deep temporal artery (pDTA), and middle temporal artery (MTA) were assessed using digital subtraction angiography and MR angiography performed 6 months or more after surgery.RESULTSSS significantly reduced the temporalis muscle thickness from 12.1 ± 5.0 mm to 7.1 ± 3.0 mm (p < 0.01). Neurological deterioration due to the swollen temporalis muscle developed in 4 of the 13 hemispheres without SS (cerebral infarction in 1, reversible neurological deficit in 2, and convulsion in 1) but in none with SS. There were no significant differences in the postoperative collateral developments of the aDTA, pDTA, and MTA between hemispheres with and without SS. The MTA more frequently developed in hemispheres with EMS in which the posterior part of the muscle was used (30/37) than those in which this part was not used (4/16) (p < 0.01).CONCLUSIONSSS of the temporalis muscle might prevent neurological deterioration caused by the swollen temporalis muscle by reducing its volume without inhibiting the development of the collateral vessels.

Comparing intracerebral hemorrhages associated with direct oral anticoagulants or warfarin.

OBJECTIVES: This cross-sectional survey explored the characteristics and outcomes of direct oral anticoagulant (DOAC)-associated nontraumatic intracerebral hemorrhages (ICHs) by analyzing a large nationwide Japanese discharge database. METHODS: We analyzed data from 2,245 patients who experienced ICHs while taking anticoagulants (DOAC: 227; warfarin: 2,018) and were urgently hospitalized at 621 institutions in Japan between April 2010 and March 2015. We compared the DOAC- and warfarin-treated patients based on their backgrounds, ICH severities, antiplatelet therapies at admission, hematoma removal surgeries, reversal agents, mortality rates, and modified Rankin Scale scores at discharge. RESULTS: DOAC-associated ICHs were less likely to cause moderately or severely impaired consciousness (DOAC-associated ICHs: 31.3%; warfarin-associated ICHs: 39.4%; p = 0.002) or require surgical removal (DOAC-associated ICHs: 5.3%; warfarin-associated ICHs: 9.9%; p = 0.024) in the univariate analysis. Propensity score analysis revealed that patients with DOAC-associated ICHs also exhibited lower mortality rates within 1 day (odds ratio [OR] 4.96, p = 0.005), within 7 days (OR 2.29, p = 0.037), and during hospitalization (OR 1.96, p = 0.039). CONCLUSIONS: This nationwide study revealed that DOAC-treated patients had less severe ICHs and lower mortality rates than did warfarin-treated patients, probably due to milder hemorrhages at admission and lower hematoma expansion frequencies.