Biology subjects

Mills, D. J.

Publications and source records attributed to Mills, D. J..

6 recordsLinked to original sources

bioRxiv2023

Undergraduates' reactions to errors mediates the association between growth mindset and study strategies

BackgroundStudents employ a variety of study strategies to learn and master content in their courses. Strategies vary widely in their effectiveness for promoting deep, long-term learning, yet most students use ineffective strategies frequently. Efforts to educate students about effective study strategies have revealed that knowledge about effective strategies is by itself insufficient for encouraging widespread and lasting changes. An important next step is to uncover factors that influence the decisions students make about study strategy use. We explored the association between beliefs about intelligence (mindset, universality, and brilliance) and study strategies. The most effective study strategies are error-prone, and beliefs about intelligence carry implications for whether errors are a normal and even beneficial part of the learning process (e.g., growth mindset) or signs of insufficient intelligence (e.g., fixed mindset). Therefore, we hypothesized that beliefs about and reactions to errors would mediate a relationship between beliefs about intelligence and study strategies. We tested this hypothesis by surveying 345 undergraduates enrolled in an introductory biology class at a public, research-active university in northwestern United States. ResultsConfirmatory factor analysis indicated that the internal structure of all measures functioned as expected in our sample. We fit a structural equation model to evaluate our hypothesized model. We found that mindset, but not universality nor brilliance, predicts variance in both beliefs about errors and reactions to errors. In turn, adaptive reactions to errors (but not beliefs about errors) are associated with the use of highly effective study strategies and spacing study sessions. There was a significant indirect relationship between growth mindset and spacing of study sessions. ConclusionsOur results provide evidence for a mechanism explaining the association between students mindset beliefs and academic outcomes: believing that intelligence is improvable is associated with more adaptive reactions to making errors, which correlates with choosing more error-prone and therefore more effective study strategies. Future interventions aimed at improving students study strategies may be more effective if they simultaneously target reacting adaptively to errors and emphasize that intelligence is improvable.

scientific communication and education↗

bioRxiv2021

Ca2+-mediated higher-order assembly of b0,+AT-rBAT is a key step for system b0,+ biogenesis and cystinuria

Cystinuria is a genetic disorder characterized by overexcretion of dibasic amino acids and cystine, which causes recurrent kidney stones and occasionally severe kidney failure. Mutations of the two responsible proteins, rBAT and b0,+AT, which comprise system b0,+, are linked to type I and non-type I cystinuria respectively and they exhibit distinct phenotypes due to protein trafficking defects or catalytic inactivation. Although recent structural insights into human b0,+AT-rBAT suggested a model for transport-inactivating mutations, the mechanisms by which type I mutations trigger trafficking deficiencies are not well understood. Here, using electron cryo-microscopy and biochemistry, we discover that Ca2+-mediated higher-order assembly of system b0,+ is the key to its trafficking on the cell surface. We show that Ca2+ stabilizes the interface between two rBAT molecules to mediate super-dimerization, and this in turn facilitates the N-glycan maturation of system b0,+. A common cystinuria mutant T216M and mutations that disrupt the Ca2+ site in rBAT cause the loss of higher-order assemblies, resulting in protein trafficking deficiency. Mutations at the super-dimer interface reproduce the mis-trafficking phenotype, demonstrating that super-dimerization is essential for cellular function. Cell-based transport assays confirmed the importance of the Ca2+ site and super-dimerization, and additionally suggested which residues are involved in cationic amino acid recognition. Taken together, our results provide the molecular basis of type I cystinuria and serve as a guide to develop new therapeutic strategies against it. More broadly, our findings reveal an unprecedented link between transporter oligomeric assembly and trafficking diseases in general.

biochemistry↗

bioRxiv2021

Structure of the hexameric fungal plasma membrane proton pump in its auto-inhibited state

The fungal plasma membrane H+-ATPase Pma1 is a vital enzyme, generating a proton-motive force that drives the import of essential nutrients. Auto-inhibited Pma1 hexamers in starving fungi are activated by glucose signalling resulting in phosphorylation of the auto-inhibitory domain. As related P-type ATPases are not known to oligomerise, the physiological relevance of Pma1 hexamers remains unknown. We have determined the structure of hexameric Pma1 from Neurospora crassa by cryo-EM at 3.3 [A] resolution, elucidating the molecular basis for hexamer formation and auto-inhibition, and providing a basis for structure-based drug development. Coarse-grained molecular dynamics simulations in a lipid bilayer suggest lipid-mediated contacts between monomers and a substantial protein-induced membrane deformation that could act as a proton-attracting funnel.

biochemistry↗

bioRxiv2021

High-resolution structure and dynamics of mitochondrial complex I - insights into the proton pumping mechanism

Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is a 1 MDa membrane protein complex with a central role in energy metabolism. Redox-driven proton translocation by complex I contributes substantially to the proton motive force that drives ATP synthase. Several structures of complex I from bacteria and mitochondria have been determined but its catalytic mechanism has remained controversial. We here present the cryo-EM structure of complex I from Yarrowia lipolytica at 2.1 [A] resolution, which reveals the positions of more than 1600 protein-bound water molecules, of which [~]100 are located in putative proton translocation pathways. Another structure of the same complex under steady-state activity conditions at 3.4 [A] resolution indicates conformational transitions that we associate with proton injection into the central hydrophilic axis. By combining high-resolution structural data with site-directed mutagenesis and large-scale molecular dynamics simulations, we define details of the proton translocation pathways, and offer new insights into the redox-coupled proton pumping mechanism of complex I.

biochemistry↗

bioRxiv2020

Cryo-EM structure of Helicobacter pylori urease with a novel inhibitor in the active site at 2.0 A resolution

Infection of the human stomach by Helicobacter pylori remains a worldwide problem and greatly contributes to peptic ulcer disease and gastric cancer. Without active intervention approximately 50% of the world population will continue to be infected with this gastric pathogen. Current eradication, called triple therapy, entails a proton-pump inhibitor and two broadband antibiotics, however resistance to either clarithromycin or metronidazole is greater than 25% and rising. Therefore, there is an urgent need for a targeted, high-specificity eradication drug. Gastric infection by H. pylori depends on the expression of a nickeldependent urease in the cytoplasm of the bacteria. Here, we report the 2.01 [A] resolution structure of the 1.1 MDa urease in complex with a novel inhibitor by cryo-electron microscopy and compare it to a {beta}-mercaptoethanol-inhibited structure at 2.45 [A] resolution. The structural information is of sufficient detail to aid in the development of inhibitors with high specificity and affinity.

cancer biology↗

bioRxiv2019

Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F1-Fo coupling

F1Fo-ATP synthases play a central role in cellular metabolism, making the energy of the proton-motive force across a membrane available for a large number of energy-consuming processes. We determined the single-particle cryo-EM structure of active dimeric ATP synthase from mitochondria of Polytomella sp. at 2.7- 2.8 [A] resolution. Separation of 13 well-defined rotary substates by 3D classification provides a detailed picture of the molecular motions that accompany c-ring rotation and result in ATP synthesis. Crucially, the F1 head rotates along with the central stalk and c-ring rotor for the first ~30{degrees} of each 120{degrees} primary rotary step. The joint movement facilitates flexible coupling of the stoichiometrically mismatched F1 and Fo subcomplexes. Flexibility is mediated primarily by the interdomain hinge of the conserved OSCP subunit, a well-established target of physiologically important inhibitors. Our maps provide atomic detail of the c-ring/a-subunit interface in the membrane, where protonation and deprotonation of c-ring cGlu111 drives rotary catalysis. An essential histidine residue in the lumenal proton access channel binds a strong non-peptide density assigned to a metal ion that may facilitate c-ring protonation, as its coordination geometry changes with c-ring rotation. We resolve ordered water molecules in the proton access and release channels and at the gating aArg239 that is critical in all rotary ATPases. We identify the previously unknown ASA10 subunit and present complete de novo atomic models of subunits ASA1-10, which make up the two interlinked peripheral stalks that stabilize the Polytomella ATP synthase dimer.

biochemistry↗