Mutation at the entrance of the quinone cavity severely disrupts quinone binding in respiratory complex I.

In all resolved structures of complex I, there exists a tunnel-like Q-chamber for ubiquinone binding and reduction. The entrance to the Q-chamber in ND1 subunit forms a narrow bottleneck, which is rather tight and requires thermal conformational changes for ubiquinone to get in and out of the binding chamber. The substitution of alanine with threonine at the bottleneck (AlaThr MUT), associated with 3460/ND1 mtDNA mutation in human complex I, is implicated in Leber's Hereditary Optic Neuropathy (LHON). Here, we show the AlaThr MUT further narrows the Q-chamber entrance cross-section area by almost 30%, increasing the activation free energy barrier of quinone passage by approximately 5 kJ mol-1. This severely disrupts quinone binding and reduction as quinone passage through the bottleneck is slowed down almost tenfold. Our estimate of the increase in free energy barrier is entirely due to the bottleneck narrowing, leading to a reduction of the transition state entropy between WT and MUT, and thus more difficult quinone passage. Additionally, we investigate details of possible water exchange between the Q-chamber and membrane. We find water exchange is dynamic in WT but may be severely slowed in MUT. We propose that LHON symptoms caused by 3460/ND1 mtDNA mutation are due to slowed quinone binding. This leads to an increased production of reactive oxidative species due to upstream electron backup at the FMN site of complex I, thus resulting in a mt bioenergetic defect.

Activation of H2O Tailored by Interfacial Electronic States at a Nanoscale Interface for Enhanced Electrocatalytic Hydrogen Evolution.

Despite the fundamental and practical significance of the hydrogen evolution reaction (HER), the reaction kinetics at the molecular level are not well-understood, especially in basic media. Here, with ZIF-67-derived Co-based carbon frameworks (Co/NCs) as model catalysts, we systematically investigated the effects of different reaction parameters on the HER kinetics and discovered that the HER activity was directly dependent not on the type of nitrogen in the carbon framework but on the relative content of surface hydroxyl and water (OH-/H2O) adsorbed on Co active sites embedded in carbon frameworks. When the ratio of the OH-/H2O was close to 1:1, the Co/NC nanocatalyst showed the best reaction performance under the condition of high-pH electrolytes, e.g., an overpotential of only 232 mV at a current density of 10 mA cm-2 in the 1 M KOH electrolyte. We unambiguously identified that the structural water molecules (SWs) in the form of hydrous hydroxyl complexes absorbed on metal centers {OHad·H2O@M+} were catalytic active sites for the enhanced HER, where M+ could be transition or alkaline metal cations. Different from the traditional hydrogen bonding of water, the hydroxyl (hydroxide) groups and water molecules in the SWs were mainly bonded together via the spatial interaction between the p orbitals of O atoms, exhibiting features of a delocalized π-bond with a metastable state. These newly formed surface bonds or transitory states could be new weak interactions that synergistically promote both interfacial electron transfer and the activation of water (dissociation of O-H bonds) at the electrode surface, i.e., the formation of activated H adducts (H*). The capture of new surface states not only explains pH-, cation-, and transition-metal-dependent hydrogen evolution kinetics but also provides completely new insights into the understanding of other electrocatalytic reductions involving other small molecules, including CO2, CO, and N2.

Mechanical Allosteric Couplings of Redox-Induced Conformational Changes in Respiratory Complex I.

We apply linear response theory to calculate mechanical allosteric couplings in respiratory complex I between the iron sulfur cluster N2, located in the catalytic cavity, and the membrane part of the enzyme, separated from it by more than 50 Å. According to our hypothesis, the redox reaction of ubiquinone in the catalytic cavity of the enzyme generates an unbalanced charge that via repulsion of the charged redox center N2 produces local mechanical stress that transmits into the membrane part of the enzyme where it induces proton pumping. Using coarse-grained simulations of the enzyme, we calculated mechanistic allosteric couplings that reveal the pathways of the mechanical transmission of the stress along the enzyme. The results shed light on the recent experimental studies where a stabilization of the enzyme with an introduced disulfide bridge resulted in the abolishing of proton pumping. Simulation of the disulfide bond action indicates a dramatic change of the mechanistic coupling pathways in line with experimental findings.

Quinone binding in respiratory complex I: Going through the eye of a needle. The squeeze-in mechanism of passing the narrow entrance of the quinone site.

At the joint between the membrane and hydrophilic arms of the enzyme, the structure of the respiratory complex I reveals a tunnel-like Q-chamber for ubiquinone binding and reduction. The narrow entrance of the quinone chamber located in ND1 subunit forms a bottleneck (eye of a needle) which in all resolved structures was shown to be too small for a bulky quinone to pass through, and it was suggested that a conformational change is required to open the channel. The closed bottleneck appears to be a well-established feature of all structures reported so-far, both for the so-called open and closed states of the enzyme, with no indication of a stable open state of the bottleneck. We propose a squeeze-in mechanism of the bottleneck passage, where dynamic thermal conformational fluctuations allow quinone to get in and out. Here, using molecular dynamics simulations of the bacterial enzyme, we have identified collective conformational changes that open the quinone chamber bottleneck. The model predicts a significant reduction-due to a need for a rare opening of the bottleneck-of the effective bi-molecular rate constant, in line with the available kinetic data. We discuss possible reasons for such a tight control of the quinone passage into the binding chamber and mechanistic consequences for the quinone two-electron reduction.

Physical Origin of Dual-Emission of Au-Ag Bimetallic Nanoclusters.

On the origin of photoluminescence of noble metal NCs, there are always hot debates: metal-centered quantum-size confinement effect VS ligand-centered surface state mechanism. Herein, we provided solid evidence that structural water molecules (SWs) confined in the nanocavity formed by surface-protective-ligand packing on the metal NCs are the real luminescent emitters of Au-Ag bimetal NCs. The Ag cation mediated Au-Ag bimetal NCs exhibit the unique pH-dependent dual-emission characteristic with larger Stokes shift up to 200 nm, which could be used as potential ratiometric nanosensors for pH detection. Our results provide a completely new insight on the understanding of the origin of photoluminescence of metal NCs, which elucidates the abnormal PL emission phenomena, including solvent effect, pH-dependent behavior, surface ligand effect, multiple emitter centers, and large-Stoke's shift.

Respiratory complex I: Bottleneck at the entrance of quinone site requires conformational change for its opening.

The structure of the entire respiratory complex I is now known at reasonably high resolution for many species - bacteria, yeast, and several mammals, including human. The structure reveals an almost 30 angstrom tunnel-like chamber for ubiquinone binding in the core part of the enzyme, at the joint between the membrane and hydrophilic arms of the enzyme. Here we characterize the geometric bottleneck forming the entrance of the quinone reaction chamber. Computer simulations of quinone/quinol passage through the bottleneck suggest that in all structures available, from bacterial to human, this bottleneck is too narrow for the quinone or quinol to pass and that a conformational change is required to open the channel. Moreover, the bottleneck is too narrow even for isoprenoid tail free passage. The closed structure can be an artifact of the crystallization packing forces, low temperature, or other unnatural conditions occurring in the structural data acquisition procedure that affect this flexible part of the enzyme. Two of the helices forming the bottleneck are in direct contact with the subunit (ND3) that was recently demonstrated to be involved in conformational changes during the redox proton pumping cycle, which indicates flexibility of that part of the enzyme. We conclude that the published structures are all locked in the unfunctional states and do not represent correctly the functional enzyme; we discuss possible ways to open the structure in the context of possible mechanisms of the enzyme.