To understand how signaling proteins function, it is crucial to know the time-ordered sequence of events that lead state. We recently developed on BioCARS 14-IDB beamline at Advanced Photon Source infrastructure required characterize structural changes in protein crystals with near-atomic spatial resolution and 150-ps time resolution, have used this capability track reversible photocycle photoactive yellow (PYP) following trans-to-cis photoisomerization its p-coumaric acid (pCA) chromophore...

The second law of thermodynamics is a powerful imperative that has acquired several expressions during the past centuries. Connections between two its most prominent forms, i.e. evolutionary principle by natural selection and least action, are examined. Although no fundamentally new findings provided, it illuminating to see how principles rationalizing motions reconcile one law. law, when written as differential equation motion, describes evolution along steepest descents in energy and,...

Significance Complex I is a redox-driven proton pump, central for aerobic energy transduction. We show here by large-scale quantum and classical molecular simulations how reduction of quinone (Q) in the hydrophilic domain complex activates pump membrane domain. Our indicate that Q leads to local charge redistributions trigger conformational changes via an array alternating charged residues domain, nearly 40 Å away. These mechanistic observations are supported site-directed mutagenesis key...

Quantum chemical calculations are important for elucidating light-capturing mechanisms in photobiological systems. The time-dependent density functional theory (TDDFT) has become a popular methodology because of its balance between accuracy and computational scaling, despite problems describing, example, charge transfer states. As step toward systematically understanding the performance TDDFT on biomolecular systems, we study here 17 commonly used functionals, including seven long-range...

Significance Using large-scale classical and quantum simulations, we elucidate key aspects of the molecular function complex I, a protein central to biological energy conversion. Complex I serves as primary electron entry point into mitochondrial bacterial respiratory chains operates redox-coupled proton pump. Our simulations suggest that transient water establish highly efficient pathways for transfer. findings form basis understanding long-range conversion in mechanistic similarities other...

Significance Complex I is a redox-driven proton pump, central to aerobic energy conversion in most living organisms. To elucidate the mechanism of its pumping machinery, we need detailed molecular picture how access across membrane established and regulated. In this work find that pathways complex form at symmetry-related locations near broken transmembrane helices. The channel opening allows influx water molecules, catalyzing rapid Grotthuss-type transfer reactions. hydration these channels...

Significance Complex I is the primary energy-converting enzyme of aerobic respiratory chains. By reducing quinone to quinol, this gigantic pumps protons across its membrane domain, which in turn powers ATP synthesis and active transport. Despite recently resolved molecular structures complex I, dynamics coupling pumping function remains unclear. Here we show by large-scale simulations that reduction leads ejection quinol molecule from site into a second binding near proton-pumping domain I....

Significance Respiratory complex I, a redox-coupled proton pumping enzyme, is central to aerobic metabolism in mammalian mitochondria and implicated many neuromuscular disorders. One of its substrates, ubiquinone-10, binds an unusually long narrow channel, which at the intersection enzyme’s electron transfer modules hotspot for disease-causing mutations. Here, we use minimal, self-assembled respiratory chain study I catalyzing with ubiquinones different isoprenoid lengths. We show that...

Abstract Respiratory complex I (NADH:ubiquinone oxidoreductase) captures the free energy from oxidising NADH and reducing ubiquinone to drive protons across mitochondrial inner membrane power oxidative phosphorylation. Recent cryo-EM analyses have produced near-complete models of mammalian complex, but leave molecular principles its long-range coupling mechanism open debate. Here, we describe 3.0-Å resolution structure mouse heart mitochondria with a substrate-like inhibitor, piericidin A,...

Cardiolipin modulates the activity of membrane-bound respiratory enzymes that catalyze biological energy transduction. The complex I functions as primary redox-driven proton pump in mitochondrial and bacterial chains, its is strongly enhanced by cardiolipin. However, despite recent advances structural biology I, cardiolipin-specific interaction mechanisms currently remain unknown. On basis millisecond molecular simulations, we suggest cardiolipin binds to proton-pumping subunits induces...

Abstract Synthetic lipid membranes have served as important models for cellular membranes. However, these static do not recapitulate the dynamic nature of biological which are frequently remodeled to support function. An ideal membrane model would thus also display exchange lipids. In this work, we achieve such a system by coupling self‐assembly peptides into with chemical reaction cycle. The cycle activates and deactivates at expense fuel. resulting dynamically remodeled, and, over their 40...

In biology, self-assembly of proteins and energy-consuming reaction cycles are intricately coupled. For example, tubulin is activated deactivated for assembly by a guanosine triphosphate (GTP)-driven cycle, the emerging microtubules catalyze this cycle changing microenvironment tubulin. Recently, synthetic analogs chemically fueled assemblies have emerged, but examples in which reciprocally coupled remain rare. work, we report peptide that can be self-assembly. The change their building...

Abstract The heat shock protein 90 (Hsp90) is a molecular chaperone that employs the free energy of ATP hydrolysis to control folding and activation several client proteins in eukaryotic cell. To elucidate how local ATPase reaction active site couples global conformational dynamics Hsp90, we integrate here large-scale simulations with biophysical experiments. We show switching conserved ion pairs between N-terminal domain, harbouring site, middle domain strongly modulates catalytic barrier...

Abstract Photosynthetic organisms capture light energy to drive their metabolism, and employ the chemical reducing power convert carbon dioxide (CO 2 ) into organic molecules. Photorespiration, however, significantly reduces photosynthetic yields. To survive under low CO concentrations, cyanobacteria evolved unique carbon-concentration mechanisms that enhance efficiency of fixation, for which molecular principles have remained unknown. We show here how modular adaptations enabled...

Photosystem II (PSII) catalyzes light-driven water oxidization, releasing O2 into the atmosphere and transferring electrons for synthesis of biomass. However, despite decades structural functional studies, oxidation mechanism PSII has remained puzzling a major challenge modern chemical research. Here, we show that redox-triggered proton transfer between its oxygen-evolving Mn4O5Ca cluster nearby conserved buried ion-pairs, which are connected to bulk solvent via pathway. By using multi-scale...

Electron bifurcation is a fundamental energy coupling mechanism widespread in microorganisms that thrive under anoxic conditions. These organisms employ hydrogen to reduce CO2, but the molecular mechanisms have remained enigmatic. The key enzyme responsible for powering these thermodynamically challenging reactions electron-bifurcating [FeFe]-hydrogenase HydABC reduces low-potential ferredoxins (Fd) by oxidizing gas (H2). By combining single-particle cryo-electron microscopy (cryoEM)...

Recent breakthroughs in neural network-based structure prediction methods, such as AlphaFold2 and RoseTTAFold, have dramatically improved the quality of computational protein prediction. These models also provide statistical confidence scores that can estimate uncertainties predicted structures, but it remains unclear to what extent these are related intrinsic conformational dynamics proteins. Here, we compare with explicit large-scale molecular simulations 28 one- two-domain proteins...

Complex I is a redox-driven proton pump that drives electron transport chains and powers oxidative phosphorylation across all domains of life. Yet, despite recently resolved structures from multiple organisms, it still remains unclear how the redox reactions in trigger pumping up to 200 Å away active site. Here, we show proton-coupled transfer during quinone reduction drive long-range conformational changes conserved loops trans-membrane (TM) helices membrane domain Yarrowia lipolytica. We...