Evolution of a self-renewing, participant-centered workshop series in BMB assessment.

We present as a case study the evolution of a series of participant-centered workshops designed to meet a need in the life sciences education community-the incorporation of best practices in the assessment of student learning. Initially, the ICABL (Inclusive Community for the Assessment of Biochemistry and Molecular Biology/BMB Learning) project arose from a grass-roots effort to develop material for a national exam in biochemistry and molecular biology. ICABL has since evolved into a community of practice in which participants themselves-through extensive peer review and reflection-become integral stakeholders in the workshops. To examine this evolution, this case study begins with a pilot workshop supported by seed funding and thoughtful programmatic assessment, the results of which informed evidence-based changes that, in turn, led to an improved experience for the community. Using participant response data, the case study also reveals critical features for successful workshops, including participant-centered activities and the value of frequent peer review of participants' products. Furthermore, we outline a train-the-trainer model for creating a self-renewing community by bringing new perspectives and voices into an existing core leadership team. This case study, then, offers a blueprint for building a thriving, evolving community of practice that not only serves the needs of individual scientist-educators as they seek to enhance student learning, but also provides a pathway for elevating members to positions of leadership.

Investigating the Roles of Active Site Residues in Mycobacterium tuberculosis Indole-3-glycerol Phosphate Synthase, a Potential Target for Antitubercular Agents.

Mycobacterium tuberculosis drug resistance is emerging and new drug targets are needed. Tryptophan biosynthesis is necessary for M. tuberculosis replication and virulence. Indole-3-glycerol phosphate synthase (IGPS) catalyzes a step in M. tuberculosis tryptophan biosynthesis and has been suggested as a potential anti-infective target, but our understanding of this enzyme is limited. To aid in inhibitor design and gain a greater mechanistic picture of this enzyme, there is a need to understand the roles of active site amino acids in ligand binding and catalysis. In this work, we explored the roles of conserved active site amino acids Glu57, Lys59, Lys119, Glu168, and Glu219. Mutation of each to Ala results in loss of all detectable activity. The Glu57Gln, Lys59Arg, Lys119Arg, Glu168Gln, and Glu219Asp mutations result in large activity losses, while Glu219Gln has enhanced activity. Analysis of the enzymatic data yields the following main conclusions: (A) Lys119 is the likely catalytic acid in the CdRP ring closure step. (B) Glu168 stabilizes a charged reaction intermediate and may also be the catalytic base. (C) Glu57, Glu219, and Lys119 form a closely arranged triad in which Glu57 and Glu219 modulate the pKa of Lys119, and thus overall activity. This increased understanding of inter- and intramolecular interactions and demonstration of the highly coordinated nature of the M. tuberculosis IGPS active site provide new mechanistic information and guidance for future work with this potential new drug target.

Multi-technique structural analysis of zinc carboxylates (soaps).

A series of medium- and long-chain zinc carboxylates (zinc octanoate, zinc nonanoate, zinc decanoate, zinc undecanoate, zinc dodecanoate, zinc pivalate, zinc stearate, zinc palmitate, zinc oleate, and zinc azelate) was analyzed by ultra-high-field 67Zn NMR spectroscopy up to 35.2 T, as well as 13C NMR and FTIR spectroscopy. We also report the single-crystal X-ray diffraction structures of zinc nonanoate, zinc decanoate, and zinc oleate-the first long-chain carboxylate single-crystals to be reported for zinc. The NMR and X-ray diffraction data suggest that the carboxylates exist in three distinct geometric groups, based on structural and spectroscopic parameters. The ssNMR results presented here present a future for dynamic nuclear polarization (DNP)-NMR-based minimally invasive methods for testing artwork for the presence of zinc carboxylates.

Mutational analysis confirms the presence of distal inhibitor-selectivity determining residues in B. stearothermophilus dihydrofolate reductase.

Many antibacterial and antiparasitic drugs work by competitively inhibiting dihydrofolate reductase (DHFR), a vital enzyme in folate metabolism. The interactions between inhibitors and DHFR active site residues are known in many homologs but the contributions from distal residues are less understood. Identifying distal residues that aid in inhibitor binding can improve targeted drug development programs by accounting for distant influences that may be less conserved and subject to frequent resistance causing mutations. Previously, a novel, homology-based, computational approach that mines ligand inhibition data was used to predict residues involved in inhibitor selectivity in the DHFR family. Expectedly, some inhibitor selectivity determining residue positions were predicted to lie in the active site and coincide with experimentally known inhibitor selectivity determining positions. However, other residues that group spatially in clusters distal to the active site have not been previously investigated. In this study, the effect of introducing amino acid substitutions at one of these predicted clusters (His38-Ala39-Ile40) on the inhibitor selectivity profile in Bacillus stearothermophilus dihydrofolate reductase (Bs DHFR) was investigated. Mutations were introduced into these cluster positions to change sidechain chemistry and size. We determined kcat and KM values and measured KD values at equilibrium for two competitive DHFR inhibitors, trimethoprim (TMP) and pyrimethamine (PYR). Mutations in the His38-Ala39-Ile40 cluster significantly impacted inhibitor binding and TMP/PYR selectivity - seven out of nine mutations resulted in tighter binding to PYR when compared to TMP. These data suggest that the His38-Ala39-Ile40 cluster is a distal inhibitor selectivity determining region that favors PYR binding in Bs DHFR and, possibly, throughout the DHFR family.

Review of the use of NMR spectroscopy to investigate structure, reactivity, and dynamics of lead soap formation in paintings.

Heavy metal carboxylate or soap formation is a widespread deterioration problem affecting oil paintings and other works of art bearing oil-based media. Lead soaps are prevalent in traditional oil paintings because lead white was the white pigment most frequently chosen by old masters for the paints and in some cases for the ground preparations, until the development of other white pigments from approximately the middle of the 18th century on, and because of the wide use of lead-tin yellow. In the latter part of the 19th century, lead white began to be replaced by zinc white. The factors that influence soap formation have been the focus of intense study starting in the late 1990s. Since 2014, nuclear magnetic resonance (NMR) studies have contributed a unique perspective on the issue by providing chemical, structural, and dynamic information about the species involved in the process, as well as the effects of environmental conditions such as relative humidity and temperature on the kinetics of the reaction(s). In this review, we explore recent insights into soap formation gained through solid-state NMR and single-sided NMR techniques.

Water Diffusion and Transport in Oil Paints as Studied by Unilateral NMR and 1 H High-Resolution MAS-NMR Spectroscopy.

Heavy metal carboxylate degradation severely affects thousands of oil paintings. Relative humidity has been reported to accelerate the rate of the reactions. To evaluate its role further, water diffusion and molecular mobility of protons in linseed oil-based lead white paints were studied by unilateral NMR and 1 H HRMAS spectroscopy. The results indicate that exposure to high %RH for relatively long times affects the dynamics of the oil paint's mobile fraction and that the effect is more pronounced as the thickness of the film increases. It was found that the paint can absorb appreciable amounts of water and has a porosity of approximately 6 % available for the diffusion of water, for which a regime of restricted diffusion was observed. Furthermore, the presence of bound and free-moving water, due to the possible formation of hydrated ionic-group clusters, supports the hypothesis of a polymeric/ionomeric network, as well as regions of essentially water free to move as in the bulk. The findings allow a better understanding of the role of water as a factor activating the degradation process in linseed oil-based lead white paints.

Molecular dynamics of palmitic acid and lead palmitate in cross-linked linseed oil films: Implications from deuterium magnetic resonance for lead soap formation in traditional oil paintings.

Many oil paintings, dating from the 15th century to the present, are affected by the formation of heavy-metal carboxylates (soaps) that alter the structural integrity and appearance of the works. Through transport phenomena not yet understood, free fatty acids formed from oils used as binders migrate through the paint film and react with heavy-metal ions that are constituents of pigments and/or driers, forming metal carboxylates. The local molecular dynamics of fatty acids and metal carboxylates are factors influencing material transport in these systems. We report temperature-dependent 2H NMR spectra of palmitic acid and lead palmitate as pure materials, in cross-linked linseed oil films, and in a lead white linseed oil paint film as part of our broader research into metal soap formation. Local dynamics at the α carbon, at the terminal methyl group, and at the middle of the fatty acid chain were observed in specifically deuterated materials. Changes in the dynamic behavior with temperature were observed by the appearance of two species, a solid-like material and a liquid-like material. The relative amounts of the two phases and their deuterium NMR parameters indicate that the amount of liquid-like material and the local dynamics at that site increase with temperature. At the three locations along the chain and at all temperatures, there is a larger percentage of acyl chains of both palmitic acid and lead palmitate that are "mobile" or liquid-like in linseed oil films than there are in the pure materials. However, the percentage of liquid-like species is decreased in a lead white paint film, as compared to a linseed oil matrix. In addition, these experiments indicate that there is a larger percentage of liquid-like acyl chains of palmitic acid than of lead palmitate under identical conditions in these model paint systems.

Elemental and Molecular Segregation in Oil Paintings due to Lead Soap Degradation.

The formation of Pb, Zn, and Cu carboxylates (soaps) has caused visible deterioration in hundreds of oil paintings dating from the 15th century to the present. Through transport phenomena not yet understood, free fatty acids in the oil binding medium migrate through the paint and react with pigments containing heavy metals to form soaps. To investigate the complex correlation among the elemental segregation, types of chemical compounds formed, and possible mechanisms of the reactions, a paint sample cross-section from a 15th century oil painting was examined by synchrotron X-ray techniques. X-ray fluorescence (XRF) microscopy, quantified with elemental correlation density distribution, showed Pb and Sn segregation in the soap-affected areas. X-ray absorption near edge structure (XANES) around the Pb-L3 absorption edge showed that Pb pigments and Pb soaps can be distinguished while micro-XANES gave further information on the chemical heterogeneity in the paint film. The advantages and limitations of these synchrotron-based techniques are discussed and compared to those of methods routinely used to analyze paint samples. The results presented set the stage for improving the information extracted from samples removed from works of art and for correlating observations in model paint samples to those in the naturally aged samples, to shed light onto the mechanism of soap formation.

DNP-enhanced ultrawideline 207Pb solid-state NMR spectroscopy: an application to cultural heritage science.

Dynamic nuclear polarization (DNP) is used to enhance the (ultra)wideline 207Pb solid-state NMR spectra of lead compounds of relevance in the preservation of cultural heritage objects. The DNP SSNMR experiments enabled, for the first time, the detection of the basic lead carbonate phase of the lead white pigment by 207Pb SSNMR spectroscopy. Variable-temperature experiments revealed that the short T'2 relaxation time of the basic lead carbonate phase hinders the acquisition of the NMR signal at room temperature. We additionally observe that the DNP enhancement is twice as large for lead palmitate (a lead soap, which is a degradation product implicated in the visible deterioration of lead-based oil paintings), than it is for the basic lead carbonate. This enhancement has allowed us to detect the formation of a lead soap in an aged paint film by 207Pb SSNMR spectroscopy; which may aid in the detection of deterioration products in smaller samples removed from works of art.

Coordination geometry of lead carboxylates - spectroscopic and crystallographic evidence.

Despite their versatility, only a few single-crystal X-ray structures of lead carboxylates exist, due to difficulties with solubility. In particular, the structures of long-chain metal carboxylates have not been reported. The lone electron pair in Pb(ii) can be stereochemically active or inactive, leading to two types of coordination geometries commonly referred to as hemidirected and holodirected structures, respectively. We report (13)C and (207)Pb solid-state NMR and infrared spectra for a series of lead carboxylates, ranging from lead hexanoate (C6) to lead hexadecanoate (C18). The lead carboxylates based on consistent NMR parameters can be divided in two groups, shorter-chain (C6, C7, and C8) and longer-chain (C9, C10, C11, C12, C14, C16, and C18) carboxylates. This dichotomy suggests two modes of packing in these solids, one for the short-chain lead carboxylates and one for long-chain lead carboxylates. The consistency of the (13)C and (207)Pb NMR parameters, as well as the IR data, in each group suggests that each motif represents a structure characteristic of each subgroup. We also report the single-crystal X-ray diffraction structure of lead nonanoate (C9), the first single-crystal structure to have been reported for the longer-chain subgroup. Taken together the evidence suggests that the coordination geometry of C6-C8 lead carboxylates is hemidirected, and that of C9-C14, C16 and C18 lead carboxylates is holodirected.

207Pb and 119Sn solid-state NMR and relativistic density functional theory studies of the historic pigment lead-tin yellow type I and its reactivity in oil paintings.

Lead soaps (lead carboxylates) have been detected in traditional oil paintings in layers containing the pigment lead-tin yellow type I (LTY-I). LTY-I has been used by artists from at least the second quarter of the 15th century until the first half of the 18th century. Soap formation can lead to protrusions in paint layers and increased transparency, causing the paint support to become visible. We have characterized LTY-I by (119)Sn and (207)Pb solid-state NMR (ssNMR) spectroscopy. Using a combination of NMR techniques and DFT molecular cluster calculations, we identify the individual species in LTY-I and determine their (119)Sn and (207)Pb chemical-shift tensors. The presence of starting materials from the synthesis, minium, and tin(IV) oxide was also verified. Knowledge of the chemical-shift tensor components and the impurities in LTY-I is important for examining the chemistry of degradation processes and soap formation. We demonstrate that ssNMR can be used to detect reaction between Pb2SnO4 and added palmitic acid in a model paint sample containing LTY-I.

Nuclear magnetic resonance spectra and (207)Pb chemical-shift tensors of lead carboxylates relevant to soap formation in oil paintings.

Soap formation in traditional oil paintings occurs when heavy-metal-containing pigments, such as lead white, 2PbCO3·Pb(OH)2, and lead tin yellow type I, Pb2SnO4, react with fatty acids in the binding medium. These soaps may form aggregates that can be 100-200 µm in diameter, which swell and protrude through the paint surface, resulting in the degradation of the paint film and damage to the integrity of the artwork. The factors that trigger soap formation and the mechanism(s) of the process are not yet well understood. To elucidate these issues, chemical and structural information is necessary, which can be obtained using solid-state (207)Pb and (13)C nuclear magnetic resonance (NMR). In this article, we report (207)Pb and (13)C solid-state NMR spectra and (207)Pb chemical-shift tensors of lead carboxylates implicated in soap formation: lead stearate, lead palmitate, and lead azelate, in addition to lead oleate and lead heptanoate for comparison. The (13)C cross polarization with magic-angle spinning (MAS) spectra of these lead carboxylates show resonance doubling for the carbons closest to the lead, indicating two different conformations of the fatty acid chains in the asymmetric unit. The (207)Pb NMR spectra, from which tensors were determined, were obtained with direct excitation and spin-temperature alternation, with and without MAS, and with the wide band uniform rate smooth truncation Carr-Purcell-Meiboom-Gill pulse sequence. The results of these experiments show that the local coordination environment of lead azelate is different from lead palmitate and lead stearate and could thus be distinguished from these in a paint film displaying soap formation. In addition, comparing the (207)Pb NMR chemical-shift tensors of the lead carboxylates studied shows that crystal packing of the acyl chains may be a factor in determining the coordination environment around the lead.

Structural evidence: a single charged residue affects substrate binding in cytochrome P450 BM-3.

Cytochrome P450 BM-3 is a bacterial enzyme with sequence similarity to mammalian P450s that catalyzes the hydroxylation of fatty acids with high efficiency. Enzyme-substrate binding and dynamics has been an important topic of study for cytochromes P450 because most of the crystal structures of substrate-bound structures show the complex in an inactive state. We have determined a new crystal structure for cytochrome P450 BM-3 in complex with N-palmitoylglycine (NPG), which unexpectedly showed a direct bidentate ion pair between NPG and arginine 47 (R47). We further explored the role of R47, the only charged residue in the binding pocket in cytochrome P450 BM-3, through mutagenesis and crystallographic studies. The mutations of R47 to glutamine (R47Q), glutamic acid (R47E), and lysine (R47K) were designed to investigate the role of its charge in binding and catalysis. The oppositely charged R47E mutation had the greatest effect on activity and binding. The crystal structure of R47E BMP shows that the glutamic acid side chain is blocking the entrance to the binding pocket, accounting for NPG's low binding affinity and charge repulsion. For R47Q and R47K BM-3, the mutations caused only a slight change in kcat and a large change in Km and Kd, which suggests that R47 mostly is involved in binding and that our crystal structure, 4KPA , represents an initial binding step in the P450 cycle.