Showing 41 - 50 of 59 Items

Date: 2023-01-01

Creator: Ibrahim G. Saleh

Access: Access restricted to the Bowdoin Community

Date: 2022-01-01

Creator: William J. Rackear

Access: Access restricted to the Bowdoin Community

Date: 2021-07-15

Creator: Phuong Luong, Danielle H. Dube

Access: Open access

The bacterial glycocalyx is a quintessential drug target comprised of structurally distinct glycans. Bacterial glycans bear unusual monosaccharide building blocks whose proper construction is critical for bacterial fitness, survival, and colonization in the human host. Despite their appeal as therapeutic targets, bacterial glycans are difficult to study due to the presence of rare bacterial monosaccharides that are linked and modified in atypical manners. Their structural complexity ultimately hampers their analytical characterization. This review highlights recent advances in bacterial chemical glycobiology and focuses on the development of chemical tools to probe, perturb, and image bacterial glycans and their biosynthesis. Current technologies have enabled the study of bacterial glycosylation machinery even in the absence of detailed structural information.

Date: 2001-06-09

Creator: D. J. Sutton, Z. J. Kabala, A. Francisco, D. Vasudevan

Access: Open access

We conducted chemical characterization, batch, column, and modeling studies to elucidate the sorption and transport of rhodamine WT (RWT) in the subsurface. The sand-pack material from the Lizzie field site near Greenville, North Carolina, served as our porous media. Our study confirms earlier results that RWT consists of two isomers with different sorption properties. It also shows that the two isomers have distinct emission spectra and are equally distributed in the RWT solution. The presence of the two isomers with different sorption properties and distinct emission spectra introduces an error in measuring the RWT concentration with fluorometers during porous media tracer studies. The two isomers become chromatographically separated during transport and thus arrive in a different concentration ratio than that of the RWT solutions used for fluorometer calibration and test injection. We found that this groundwater tracer chromatographic error could be as high as 7.8%. We fit six different reactive-solute transport models of varying complexity to our four column experiments. A two-solute, two-site sorption transport model that accounts for nonequilibrium sorption accurately describes the breakthrough curves of the shorter-timescale column experiments. However, possibly due to the groundwater tracer chromatographic error we discovered, this model, or a similar one that accounts for a Freundlich isotherm for one of the solutes, fails to describe the RWT transport in the longer-timescale column experiments. The presence of the two RWT isomers may complicate the interpretation of field tracer tests because a shoulder, or any two peaks in a breakthrough curve, could result from either aquifer heterogeneity or the different arrival times of the two isomers. In cases where isomer 2 sorbs to such an extent that its breakthrough is not recorded during a test, only isomer 1 is measured, and therefore only 50% of the injected mass is recorded. Isomer 1 of RWT can be accurately modeled with a one-solute, two-site, nonequilibrium sorption model. This conclusion and the results from our batch studies suggest that RWT isomer 1 is an effective groundwater tracer but that the presence of isomer 2 hampers its effectiveness.

Date: 2023-01-01

Creator: Seamus Frey

Access: Access restricted to the Bowdoin Community

• Embargo End Date: 2027-05-16

Date: 2024-01-01

Creator: Morgan Adams

Access: Embargoed

Date: 2020-01-01

Creator: Thomas Regan

Access: Access restricted to the Bowdoin Community

Date: 2005-09-02

Creator: Anne E. McBride, Jeffrey T. Cook, Elizabeth A. Stemmler, Kate L. Rutledge, Kelly A., McGrath, Jeffrey A. Rubens

Access: Open access

Arginine methylation can affect both nucleocytoplasmic transport and protein-protein interactions of RNA-binding proteins. These effects are seen in cells that lack the yeast hnRNP methyltransferase (HMT1), raising the question of whether effects on specific proteins are direct or indirect. The presence of multiple arginines in individual methylated proteins also raises the question of whether overall methylation or methylation of a subset of arginines affects protein function. We have used the yeast mRNA-binding protein Npl3 to address these questions in vivo. Matrix-assisted laser desorption/ionization Fourier transform mass spectrometry was used to identify 17 methylated arginines in Npl3 purified from yeast: whereas 10 Arg-Gly-Gly (RGG) tripeptides were exclusively dimethylated, variable levels off methylation were found for 5 RGG and 2 RG motif arginines. We constructed a set of Npl3 proteins in which subsets of the RGG arginines were mutated to lysine. Expression of these mutant proteins as the sole form of Npl3 specifically affected growth of a strain that requires Hmtl. Although decreased growth generally correlated with increased numbers of Arg-to-Lys mutations, lysine substitutions in the N terminus of the RGG domain showed more severe effects. Npl3 with all 15 RGG arginines mutated to lysine exited the nucleus independent of Hmtl, indicating a direct effect of methylation on Npl3 transport. These mutations also resulted in a decreased, methylation-independent interaction of Npl3 with transcription elongation factor Tho2 and inhibited Npl3 self-association. These results support a model in which arginine methylation facilitates Npl3 export directly by weakening contacts with nuclear proteins. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.

Date: 2015-09-01

Creator: Kate R. Farnham, Danielle H. Dube

Access: Open access

Here we present the development of a 13 week project-oriented biochemistry laboratory designed to introduce students to foundational biochemical techniques and then enable students to perform original research projects once they have mastered these techniques. In particular, we describe a semester-long laboratory that focuses on a biomedically relevant enzyme-Helicobacter pylori (Hp) urease-the activity of which is absolutely required for the gastric pathogen Hp to colonize the human stomach. Over the course of the semester, students undertake a biochemical purification of Hp urease, assess the success of their purification, and investigate the activity of their purified enzyme. In the final weeks of the semester, students design and implement their own experiments to study Hp urease. This laboratory provides students with an understanding of the importance of biochemistry in human health while empowering them to engage in an active area of research.

Date: 2019-01-01

Creator: Bess Vlaisavljevich, Sondre K. Schnell, Allison L. Dzubak, Kyuho Lee, Nora, Planas, Jeffrey B. Neaton, Laura Gagliardi, Berend Smit

Access: Open access

The authors regret that there are some discrepancies reproducing the data in the original article due to the determined coordinates not being the fully optimised geometries. The authors have provided more information as follows. In the manuscript entitled 'CO2 induced phase transitions in diamine-appended metal-organic frameworks', minor errors with the attached coordinates and energies reported in the paper have recently been identified. In this communication, we correct these errors. Here, we present updated optimized geometries and binding energies. We also take this opportunity to include an extended computational details section to ensure reproducibility. In addition, we show that the overall conclusions of the paper are not affected by these changes. A detailed comparison with the results reported by Lee et al.1 revealed that the DFT optimization of the coordinates provided with the manuscript do not lead to the values reported in the manuscript, and they warrant correction. Corrected coordinates and updated tables (Tables 1-7) and figures (Fig. 1, 2, 4 and 5) are included here for calculations using the PBE functional. These structures have been repeated using a slightly tighter force threshold than in the original manuscript (details below). The M06-L calculations reported in the original manuscript are not revisited since they were performed to assess the role of dispersion. Since the publication of our work in 2015, a far more detailed study of this effect has been published by one of the authors rendering these M06-L calculations unnecessary and we refer readers interested in the role of dispersion on the carbamate formation to this more recent study by Lee et al.1 In addition to correcting our DFT calculations, we examine the effects of the revised DFT values on the lattice model in this work.We recompute the lattice model with the M06-L and PBE values fromthe original manuscript as well as the corrected PBE values reported below (Fig. 6-8 and Tables 8-10). In all three sets of isotherm plots the ordering is preserved but the inflection points are spaced differently with the new PBE numbers, leading to quantitative differences that are nonetheless qualitatively similar to previous work. Finally, we discuss different ways that CO2 can coordinate to the metal binding site, as shown in Fig. 3. We should have notedmore clearly in ourmanuscript that these were starting configurations and not necessarily the final converged structures since our goal was to try several starting geometries to determine which coordination environment around the metal site was lowest in energy. Take for example bidentate insertion. Chemical intuition suggests that this structure could rotate to one that has only one CO2 oxygen center closer to the metal than the other and we observe this in our optimized structure. The resulting geometries we obtained for the starting arrangements noted in the figure are higher in energy than the chain model as reported in our original paper.We wish to emphasize that at the time of our 2015 study, our objective was to understand whether or not CO2 was bound to the metal and if one-dimensional chain formation could lead to a step in the adsorption isotherm. It has since become clear that a far more thorough study of the arrangements of the amines is required to truly understand competing amine arrangements preset in experiment. This was outside the scope of our work. Once more, these calculations are perhaps now outdated given work in the field in recent years. We again refer interested readers to a more recent study by Lee et al.1 1. Extended computational details to ensure reproducibility In the course of rectifying the error in our calculations, we wanted to ensure that all revised calculations were converged using the exact same protocol; therefore, we repeated the PBE calculations for the pair and chain models using updated computational details given here to ensure reproducibility. The M2(dobpdc) MOF contains six unsaturated metal sites per unit cell. To calculate the binding energies of CO2 in its amine appended analogue mmen-M2(dobpdc), one mmen ligand per CO2 was added per unit cell. The smaller sized ethylenediamine (en) was used to saturate the remaining amines not involved in CO2 binding. In the case of the pair mode, two mmen-amines are included per unit cell only. All DFT calculations were performed with periodic boundary conditions carried out using the VASP 5.4.4 package (original calculations were performed with VASP 5.3.3). The PBE functional was employed to examine the energetics of CO2 adsorption.3 On-site Hubbard U corrections were employed for metal d electrons.4 The U values are determined to reproduce oxidation energies in the respective metal oxides and are given in the tables below. The electron-ion interactions in these calculations were described with the projector augmented wave (PAW) method developed by Blöchl with an energy cutoff of 550 eV.5 This combination of the PBE functional, PAW scheme, and energy cutoff was used for full geometry optimization of the various species investigated until the forces on all atoms were smaller than 0.02 eV Å-1 and the SCF convergence was set to 1 × 10-7 eV. Given the large size of the unit cell and the tests with other numbers of K-points from the original study, only results obtained from G-point calculations are reported here. Finally, heats of adsorption are now reported below along with E + ZPE values, while in the original manuscript only E + ZPE were reported. No changes were made to how the vibrational corrections were computed; however, we have included some additional details to ensure reproducibility.6 Harmonic vibrational modes (ωi) were computed for CO2 in the gas phase and its bound product state (amine-CO2-MOF complex). The framework itself was taken to be rigid and only the vibrational modes associated with the motion of the amine, the metal center, first coordination sphere (oxygen atoms bound to the metal in the MOF backbone), and (if present) the bound CO2 were computed. Since the harmonic approximation breaks down for low frequency modes, we replaced all modes less than 50 cm-1 with 50 cm-1 when computing the zero-point and thermal energies. The following standard harmonic expressions were used to compute the vibrational corrections: Zero-point vibrational energy (ZPE) is: [Equation presented here] While for the bound product, the rotational and translational degrees of freedom of CO2 have been converted to additional vibrational modes allowing one to compute the thermal correction simply as: [Equation presented here] 2. Values for the chain model The chain model used in our original study included 1 mmen- and 5 en-amines. The values from the original paper are reported in Table 1. When we repeat these calculations using the procedure described in Section 1, we obtain the values in Table 2. In addition to the chain model described above (1 mmen- and 5 en-amines per unit cell), during our original study we performed calculations with another model that was not included in the manuscript since its values yielded results further from experiment. This model includes only 1 mmen-amine per unit cell (no other amines) and was used to test the assumption that the five enamines are indeed spectators with respect to the metal dependence of the binding energy. We present the results from this model in Table 3. In the original paper we noted that the energy and bond length trends are correlated and are consistent with the Irving-Williams series. This is no longer true for all metals under investigation, with Zn being an outlier. The results for Zn can be explained by more recent work.1 3. Values for the pair model The model used to compute the "pair" adsorption mechanisms included 2 mmen-amines and 0 en-amines. The values in the original paper are presented in Table 5. 4. Lattice model plots The lattice models to generate adsorption isotherms for these systems were run at one temperature (∼25 °C) using four different input parameters. First the M06-L and PBE values from the original paper were used once more as it has been some time since we have run the lattice model. Then the model is repeated with the new set of values from PBE. If we compare Fig. 7 and 8, the order is preserved, but the infliction points are spaced a bit differently. This is due to the scaling factor being constant and is something we scaled for each of the different systems as well. The slope is also a bit different, but not more then we should expect for this simple lattice model. Furthermore, we only ever aimed to reproduce the step and the order of the metals. Any finer details cannot be expected to be obtained from this model. The exact values used to compute the isotherms are given in the tables below. The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers.