Biology subjects

Pecorilla, C.

Publications and source records attributed to Pecorilla, C..

3 recordsLinked to original sources

bioRxiv2026

Molecular and Energetic Basis of Histidine Switch Dynamics in Respiratory Complex I

The respiratory complex I in mitochondria and bacteria drives the two-electron reduction of quinone to pump protons across the membrane. The molecular basis of this catalytic reaction remains enigmatic despite significant progress in structural characterization of the complex. A highly conserved histidine residue in the distal antiporter-like subunit of its membrane domain has been shown to undergo conformational changes in molecular simulations and cryo-EM structures. However, the function of histidine switch dynamics, and energetics of its conformational transitions remain unclear. Here, by applying enhanced sampling simulations, we evaluate the energetics of the histidine switch dynamics and demonstrate that it is coupled to the charge state of lysine residues ca. 10 [A] apart, which cause hydrogen bond restructuring and stabilize histidine in specific conformations. Hybrid QM/MM metadynamics simulations show that the histidine participates in gated proton transfer and may function as a proton confurcation device in complex I and related proteins. Importance of workProton pumping by the mitochondrial respiratory chain enzymes needs to be highly directional so that the ATP production occurs as efficiently as possible during high energy demands. With the protons being hard to detect by most methods of structural biology, computer simulation approaches as applied in this work offer critical information on how molecular gates within respiratory complexes can function and help elucidate the challenging questions in the field of mitochondrial bioenergetics.

biophysics↗

bioRxiv2024

Conformational dynamics of a histidine molecular switch in a cation/proton antiporter

Multisubunit Mrp type sodium proton (Na+/H+) antiporters are indispensable for the growth of alkali and salt tolerant bacteria and archaea under challenging conditions. Several subunits of the membrane protein complex are closely related to the membrane bound subunits of mitochondrial respiratory complex I, a key enzyme in aerobic energy metabolism. The molecular mechanism of ion translocation by complex I and Mrp antiporters has remained largely unknown and is the subject of intense debate. Here, we combine the power of site-directed mutagenesis and large-scale atomistic molecular dynamics simulations to elucidate the molecular basis of proton-conducting function of the MrpA subunit of the antiporter. We show that point mutations directly affect the transport activity by perturbing the conformational dynamics of a key histidine residue that acts as a molecular switch. Importantly, we find that charge and protonation state variations drive hydrogen bonding rearrangements and hydration changes, which result in coupled sidechain and backbone level conformational changes of the histidine and neighboring residues. We propose the histidine switch as a unique functional element central to proton transport function in Mrp antiporters and respiratory complex I. Significance statementEnergy conversion in biology is catalyzed by several membrane-bound enzyme complexes that drive transmembrane charge translocation. A key question is how these charges are moved against a membrane gradient in an efficient manner, i.e., what kind of gating and fail-safe mechanisms are employed by the proteins to ensure charge transfer directionality. By studying cation/proton Mrp antiporter, which shares homology with the mitochondrial complex I, we describe a conserved histidine residue acting as a molecular switch crucial for gating transfer of protons. Our work emphasizes the functional significance of conserved and conformationally mobile motifs in proteins. The results will benefit the mechanistic understanding of naturally existing proteins and design of artificial enzymes.

biophysics↗

bioRxiv2021

Structure of the stress-related LHCSR1 complex determined by an integrated computational strategy

Light-harvesting complexes (LHCs) are pigment-protein complexes whose main function is to capture sunlight and transfer the energy to reaction centers of photosystems. In response to varying light conditions, LH complexes also play photoregulation and photoprotection roles. In algae and mosses, a sub-family of LHCs, Light-Harvesting complex stress related (LHCSR), is responsible for photoprotective quenching. Despite their functional and evolutionary importance, no direct structural information on LHCSRs is available that can explain their unique properties. In this work we propose a structural model of LHCSR1 from the moss P. Patens, obtained through an integrated computational strategy that combines homology modeling, molecular dynamics, and multiscale quantum chemical calculations. The model is validated by reproducing the spectral properties of LHCSR1. Our model reveals the structural specificity of LHCSR1, as compared with the CP29 LH complex, and poses the basis for understanding photoprotective quenching in mosses.

biophysics↗