Data science and machine learning are revolutionizing enzyme engineering; however, high-throughput simulations for screening large libraries of enzyme variants remain a challenge. Here, we present a novel but highly simple approach to comparing enzyme variants with fully atomistic classical molecular dynamics (MD) simulations on a tractable timescale. Our method greatly simplifies the problem by restricting sampling only to the reaction transition state, and we show that the resulting measurements of transition-state stability are well correlated with experimental activity measurements across two highly distinct enzymes, even for mutations with effects too small to resolve with free energy methods. This method will enable atomistic simulations to achieve sampling coverage for enzyme variant prescreening and machine learning model training on a scale that was previously not possible.
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A survey on faculty perspectives on the transition to a biochemistry course-based undergraduate research experience laboratory: Transition to a CURE
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Transmembrane P 1B -type ATPase pumps catalyze the extrusion of transition metal ions across cellular lipid membranes to maintain essential cellular metal homeostasis and detoxify toxic metals. Zn( ii )-pumps of the P 1B-2 -type subclass, in addition to Zn 2+ , select diverse metals (Pb 2+ , Cd 2+ and Hg 2+ ) at their transmembrane binding site and feature promiscuous metal-dependent ATP hydrolysis in the presence of these metals. Yet, a comprehensive understanding of the transport of these metals, their relative translocation rates, and transport mechanism remain elusive. We developed a platform for the characterization of primary-active Zn( ii )-pumps in proteoliposomes to study metal selectivity, translocation events and transport mechanism in real-time, employing a “multi-probe” approach with fluorescent sensors responsive to diverse stimuli (metals, pH and membrane potential). Together with atomic-resolution investigation of cargo selection by X-ray absorption spectroscopy (XAS), we demonstrate that Zn( ii )-pumps are electrogenic uniporters that preserve the transport mechanism with 1 st -, 2 nd - and 3 rd -row transition metal substrates. Promiscuous coordination plasticity, guarantees diverse, yet defined, cargo selectivity coupled to their translocation.more » « less
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Student support programs within colleges of engineering often aim to assist students during their transition from high school to college. While studies of this transition can characterize experiences that could support the design of these support programs, research commonly focuses on the broader student population, where engineering students are often the minority. To further improve student support programs in engineering, particularly those designed for students from traditionally underrepresented populations, additional research is needed to understand the transitional experiences of first-year engineering students. The purpose of this paper is to explore the applicability of a theoretical framework from adult development (i.e., Schlossberg’s Transition Theory) to examine the high school-to-college transition of engineering students from underrepresented racial/ethnic groups. In the work-in-progress paper, we describe the theoretical constructs that appear most applicable in this context as we begin coding data from a series of three interviews with each participant. Our results will advance the engineering education community’s understanding of the applicability of Transition Theory for examining the transitions of students into engineering and inform future work.more » « less
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1002/bmb.21060
