Oxidative cyclization reagents reveal tryptophan cation-π interactions.

Methods for selective covalent modification of amino acids on proteins can enable a diverse array of applications, spanning probes and modulators of protein function to proteomics1-3. Owing to their high nucleophilicity, cysteine and lysine residues are the most common points of attachment for protein bioconjugation chemistry through acid-base reactivity3,4. Here we report a redox-based strategy for bioconjugation of tryptophan, the rarest amino acid, using oxaziridine reagents that mimic oxidative cyclization reactions in indole-based alkaloid biosynthetic pathways to achieve highly efficient and specific tryptophan labelling. We establish the broad use of this method, termed tryptophan chemical ligation by cyclization (Trp-CLiC), for selectively appending payloads to tryptophan residues on peptides and proteins with reaction rates that rival traditional click reactions and enabling global profiling of hyper-reactive tryptophan sites across whole proteomes. Notably, these reagents reveal a systematic map of tryptophan residues that participate in cation-π interactions, including functional sites that can regulate protein-mediated phase-separation processes.

Protein-Based Model for Energy Transfer between Photosynthetic Light-Harvesting Complexes Is Constructed Using a Direct Protein-Protein Conjugation Strategy.

Photosynthetic organisms utilize dynamic and complex networks of pigments bound within light-harvesting complexes to transfer solar energy from antenna complexes to reaction centers. Understanding the principles underlying the efficiency of these energy transfer processes, and how they may be incorporated into artificial light-harvesting systems, is facilitated by the construction of easily tunable model systems. We describe a protein-based model to mimic directional energy transfer between light-harvesting complexes using a circular permutant of the tobacco mosaic virus coat protein (cpTMV), which self-assembles into a 34-monomer hollow disk. Two populations of cpTMV assemblies, one labeled with donor chromophores and another labeled with acceptor chromophores, were coupled using a direct protein-protein bioconjugation method. Using potassium ferricyanide as an oxidant, assemblies containing o-aminotyrosine were activated toward the addition of assemblies containing p-aminophenylalanine. Both of these noncanonical amino acids were introduced into the cpTMV monomers through amber codon suppression. This coupling strategy has the advantages of directly, irreversibly, and site-selectively coupling donor with acceptor protein assemblies and avoids cross-reactivity with native amino acids and undesired donor-donor or acceptor-acceptor combinations. The coupled donor-acceptor model was shown to transfer energy from an antenna disk containing donor chromophores to a downstream disk containing acceptor chromophores. This model ultimately provides a controllable and modifiable platform for understanding photosynthetic interassembly energy transfer and may lead to the design of more efficient functional light-harvesting materials.

A Membrane-Associated Light-Harvesting Model is Enabled by Functionalized Assemblies of Gene-Doubled TMV Proteins.

Photosynthetic light harvesting requires efficient energy transfer within dynamic networks of light-harvesting complexes embedded within phospholipid membranes. Artificial light-harvesting models are valuable tools for understanding the structural features underpinning energy absorption and transfer within chromophore arrays. Here, a method for attaching a protein-based light-harvesting model to a planar, fluid supported lipid bilayer (SLB) is developed.  The protein model consists of the tobacco mosaic viral capsid proteins that are gene-doubled to create a tandem dimer (dTMV). Assemblies of dTMV break the facial symmetry of the double disk to allow for differentiation between the disk faces. A single reactive lysine residue is incorporated into the dTMV assemblies for the site-selective attachment of chromophores for light absorption. On the opposing dTMV face, a cysteine residue is incorporated for the bioconjugation of a peptide containing a polyhistidine tag for association with SLBs. The dual-modified dTMV complexes show significant association with SLBs and exhibit mobility on the bilayer. The techniques used herein offer a new method for protein-surface attachment and provide a platform for evaluating excited state energy transfer events in a dynamic, fully synthetic artificial light-harvesting system.

A Pilot Graduate Student-Led Near-Peer Mentorship Program for Transfer Students Provides a Supportive Network at an R1 Institution.

The undergraduate transfer process has well-documented challenges, especially for those who identify with groups historically excluded from science, technology, engineering, and mathematics (STEM) programs. Because transfer students gain later access to university networking and research opportunities than first-time-in-college students, transfer students interested in pursuing postbaccalaureate degrees in chemistry have a significantly shortened timeline in which to conduct research, a crucial component in graduate school applications. Mentorship programs have previously been instituted as effective platforms for the transfer of community cultural wealth within large institutions. We report here the design, institution, and assessment of a near-peer mentorship program for transfer students, the Transfer Student Mentorship Program (TSMP). Founded in 2020 by graduate students, the TSMP pairs incoming undergraduate transfer students with current graduate students for personalized mentorship and conducts discussion-based seminars to foster peer relationships. The transfer student participants have access to a fast-tracked networking method during their first transfer semester that can serve as a route for acquiring undergraduate research positions. Program efficacy was assessed via surveys investigating the rates of research participation and sense of belonging of transfer students. We observed that respondents that participated in the program experienced an overall improvement in these measures compared to respondents who did not. Having been entirely designed, instituted, and led by graduate students, we anticipate that this program will be highly tractable to other universities looking for actionable methods to improve their students' persistence in pursuing STEM degrees.

Characterizing Heterogeneous Mixtures of Assembled States of the Tobacco Mosaic Virus Using Charge Detection Mass Spectrometry.

The tobacco mosaic viral capsid protein (TMV) is a frequent target for derivatization for myriad applications, including drug delivery, biosensing, and light harvesting. However, solutions of the stacked disk assembly state of TMV are difficult to characterize quantitatively due to their large size and multiple assembled states. Charge detection mass spectrometry (CDMS) addresses the need to characterize heterogeneous populations of large protein complexes in solution quickly and accurately. Using CDMS, previously unobserved assembly states of TMV, including 16-monomer disks and odd-numbered disk stacks, have been characterized. We additionally employed a peptide-protein conjugation reaction in conjunction with CDMS to demonstrate that modified TMV proteins do not redistribute between disks. Finally, this technique was used to discriminate between protein complexes of near-identical mass but different configurations. We have gained a greater understanding of the behavior of TMV, a protein used across a broad variety of fields and applications, in the solution state.

Static Disorder has Dynamic Impact on Energy Transport in Biomimetic Light-Harvesting Complexes.

Despite extensive studies, many questions remain about what structural and energetic factors give rise to the remarkable energy transport efficiency of photosynthetic light-harvesting protein complexes, owing largely to the inability to synthetically control such factors in these natural systems. Herein, we demonstrate energy transfer within a biomimetic light-harvesting complex consisting of identical chromophores attached in a circular array to a protein scaffold derived from the tobacco mosaic virus coat protein. We confirm the capability of energy transport by observing ultrafast depolarization in transient absorption anisotropy measurements and a redshift in time-resolved emission spectra in these complexes. Modeling the system with kinetic Monte Carlo simulations recapitulates the observed anisotropy decays, suggesting an inter-site hopping rate as high as 1.6 ps-1. With these simulations, we identify static disorder in orientation, site energy, and degree of coupling as key remaining factors to control to achieve long-range energy transfer in these systems. We thereby establish this system as a highly promising, bottom-up model for studying long-range energy transfer in light-harvesting protein complexes.

Apodization Specific Fitting for Improved Resolution, Charge Measurement, and Data Analysis Speed in Charge Detection Mass Spectrometry.

Short-time Fourier transforms with short segment lengths are typically used to analyze single ion charge detection mass spectrometry (CDMS) data either to overcome effects of frequency shifts that may occur during the trapping period or to more precisely determine the time at which an ion changes mass or charge, or enters an unstable orbit. The short segment lengths can lead to scalloping loss unless a large number of zero-fills are used, making computational time a significant factor in real-time analysis of data. Apodization specific fitting leads to a 9-fold reduction in computation time compared to zero-filling to a similar extent of accuracy. This makes possible real-time data analysis using a standard desktop computer. Rectangular apodization leads to higher resolution than the more commonly used Gaussian or Hann apodization and makes it possible to separate ions with similar frequencies, a significant advantage for experiments in which the masses of many individual ions are measured simultaneously. Equally important is a >20% increase in S/N obtained with rectangular apodization compared to Gaussian or Hann, which directly translates to a corresponding improvement in accuracy of both charge measurements and ion energy measurements that rely on the amplitudes of the fundamental and harmonic frequencies. Combined with computing the fast Fourier transform in a lower-level language, this fitting procedure eliminates computational barriers and should enable real-time processing of CDMS data on a laptop computer.

Effects of Molecular Size on Resolution in Charge Detection Mass Spectrometry.

Instrumental resolution of Fourier transform-charge detection mass spectrometry instruments with electrostatic ion trap detection of individual ions depends on the precision with which ion energy is determined. Energy can be selected using ion optic filters or from harmonic amplitude ratios (HARs) that provide Fellgett's advantage and eliminate the necessity of ion transmission loss to improve resolution. Unlike the ion energy-filtering method, the resolution of the HAR method increases with charge (improved S/N) and thus with mass. An analysis of the HAR method with current instrumentation indicates that higher resolution can be obtained with the HAR method than the best resolution demonstrated for instruments with energy-selective optics for ions in the low MDa range and above. However, this gain is typically unrealized because the resolution obtainable with molecular systems in this mass range is limited by sample heterogeneity. This phenomenon is illustrated with both tobacco mosaic virus (0.6-2.7 MDa) and AAV9 (3.7-4.7 MDa) samples where mass spectral resolution is limited by the sample, including salt adducts, and not by instrument resolution. Nevertheless, the ratio of full to empty AAV9 capsids and the included genome mass can be accurately obtained in a few minutes from 1× PBS buffer solution and an elution buffer containing 300+ mM nonvolatile content despite extensive adduction and lower resolution. Empty and full capsids adduct similarly indicating that salts encrust the complexes during late stages of droplet evaporation and that mass shifts can be calibrated in order to obtain accurate analyte masses even from highly salty solutions.

Enzyme Activated Gold Nanoparticles for Versatile Site-Selective Bioconjugation.

A new enzymatic method is reported for constructing protein- and DNA-AuNP conjugates. The strategy relies on the initial functionalization of AuNPs with phenols, followed by activation with the enzyme tyrosinase. Using an oxidative coupling reaction, the activated phenols are coupled to proteins bearing proline, thiol, or aniline functional groups. Activated phenol-AuNPs are also conjugated to a small molecule biotin and commercially available thiol-DNA. Advantages of this approach for AuNP bioconjugation include: (1) initial formation of highly stable AuNPs that can be selectively activated with an enzyme, (2) the ability to conjugate either proteins or DNA through a diverse set of functional handles, (3) site-specific immobilization, and (4) facile conjugation that is complete within 2 h at room temperature under aqueous conditions. The enzymatic oxidative coupling on AuNPs is applied to the construction of tobacco mosaic virus (TMV)-AuNP conjugates, and energy transfer between the AuNPs and fluorophores on TMV is demonstrated.

Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism.

Prokaryotic nanocompartments, also known as encapsulins, are a recently discovered proteinaceous organelle-like compartment in prokaryotes that compartmentalize cargo enzymes. While initial studies have begun to elucidate the structure and physiological roles of encapsulins, bioinformatic evidence suggests that a great diversity of encapsulin nanocompartments remains unexplored. Here, we describe a novel encapsulin in the freshwater cyanobacterium Synechococcus elongatus PCC 7942. This nanocompartment is upregulated upon sulfate starvation and encapsulates a cysteine desulfurase enzyme via an N-terminal targeting sequence. Using cryo-electron microscopy, we have determined the structure of the nanocompartment complex to 2.2 Å resolution. Lastly, biochemical characterization of the complex demonstrated that the activity of the cysteine desulfurase is enhanced upon encapsulation. Taken together, our discovery, structural analysis, and enzymatic characterization of this prokaryotic nanocompartment provide a foundation for future studies seeking to understand the physiological role of this encapsulin in various bacteria.

Quantitative Modeling of Bis(pyridine)silver(I) Permanganate Oxidation of Hydantoin Derivatives: Guidelines for Predicting the Site of Oxidation in Complex Substrates.

The bis(pyridine)silver(I) permanganate promoted hydroxylation of diketopiperazines has served as a pivotal transformation in the synthesis of complex epipolythiodiketopiperazine alkaloids. This late-stage C-H oxidation chemistry is strategically critical to access N-acyl iminium ion intermediates necessary for nucleophilic thiolation of advanced diketopiperazines en route to potent epipolythiodiketopiperazine anticancer compounds. In this study, we develop an informative mathematical model using hydantoin derivatives as a training set of substrates by relating the relative rates of oxidation to various calculated molecular descriptors. The model prioritizes Hammett values and percent buried volume as key contributing factors in the hydantoin series while correctly predicting the experimentally observed oxidation sites in various complex diketopiperazine case studies. Thus, a method is presented by which to use simplified training molecules and resulting correlations to explain and predict reaction behavior for more complex substrates.

Designer substrate library for quantitative, predictive modeling of reaction performance.

Assessment of reaction substrate scope is often a qualitative endeavor that provides general indications of substrate sensitivity to a measured reaction outcome. Unfortunately, this field standard typically falls short of enabling the quantitative prediction of new substrates' performance. The disconnection between a reaction's development and the quantitative prediction of new substrates' behavior limits the applicative usefulness of many methodologies. Herein, we present a method by which substrate libraries can be systematically developed to enable quantitative modeling of reaction systems and the prediction of new reaction outcomes. Presented in the context of rhodium-catalyzed asymmetric transfer hydrogenation, these models quantify the molecular features that influence enantioselection and, in so doing, lend mechanistic insight to the modes of asymmetric induction.

Pd(Quinox)-Catalyzed Allylic Relay Suzuki Reactions of Secondary Homostyrenyl Tosylates via Alkene-Assisted Oxidative Addition.

Pd-catalyzed allylic relay Suzuki cross-coupling reactions of secondary alkyl tosylates, featuring a sterically-hindered oxidative addition and precise control of ß-hydride elimination, are reported. The identification of a linear free energy relationship between the relative rates of substrate consumption and the electronic nature of the substrate alkene suggests that the oxidative addition requires direct alkene involvement. A study of the effect of chain length on the reaction outcome supports a chelation-controlled oxidative addition.