Search

Understanding the fundamental reactivity of polymetallic complexes is challenging due to the complexity of their structures with many possible bond breaking and forming processes. Here, we apply ion mobility mass spectrometry coupled with density functional theory to investigate the disassembly mechanisms and energetics of a family of heterometallic rings and rotaxanes with the general formula [NH

Organisms across the natural world respond to their environment through the action of photoreceptor proteins. The vitamin B12-dependent photoreceptor, CarH, is a bacterial transcriptional regulator that controls the biosynthesis of carotenoids to protect against photo-oxidative stress. The binding of B12 to CarH monomers in the dark results in the formation of a homo-tetramer that complexes with DNA; B12 photochemistry results in tetramer dissociation, releasing DNA for transcription. Although the details of the response of CarH to light are beginning to emerge, the biophysical mechanism of B12-binding in the dark and how this drives domain assembly is poorly understood. Here – using a combination of molecular dynamics simulations, native ion mobility mass spectrometry and time-resolved spectroscopy – we reveal a complex picture that varies depending on the availability of B12. When B12 is in excess, its binding drives structural changes in CarH monomers that result in the formation of head-to-tail dimers. The structural changes that accompany these steps mean that they are rate-limiting. The dimers then rapidly combine to form tetramers. Strikingly, when B12 is scarcer, as is likely in nature, tetramers with native-like structures can form without a B12 complement to each monomer, with only one apparently required per head-to-tail dimer. We thus show how a bulky chromophore such as B12 shapes protein/protein interactions and in turn function, and how a protein can adapt to a sub-optimal availability of resources. This nuanced picture should help guide the engineering of B12-dependent photoreceptors as light-activated tools for biomedical applications., The function of the bacterial photoreceptor protein, CarH, is regulated by changes to its oligomeric state. Camacho et al. detail how binding of vitamin B12 in the dark drives assembly of the protein tetramer that in turn blocks transcription.

Activated ion mobility measurements provide insights to the stability of tertiary and quaternary structures of proteins and when coupled with dissociation strategies can delineate how the fold is disrupted. In this work, we use 213 nm photodissociation coupled with ion mobility mass spectrometry and collisional activation to probe the conformational landscape of model proteins. UVPD experiments are performed on proteins following in source activation and on collisionally activated photoproducts post ion mobility separation. For all observed conformations of cytochrome c, there is a significant increase in the UVPD fragmentation yield with the addition of collisional activation post mobility. Similar strategies are deployed with the multimeric proteins, concanavalin a, and haemoglobin. For these complexes’ CID results in ‘classical’ asymmetric charge distribution in subunit products, which when preceded by UV irradiation, yields fragments from within sub-units. Combining these strategies provides complex multidimensional datasets, rich in information, which here we mine with multivariate analysis (MVA). This approach readily determines differences in UVPD and CID fragmentation patterns as a function of conformation and reveals diagnostic information about the precursor native structure without the limitations of current methods that only assign backbone cleavage sites.

Organisms across the natural world respond to their environment through the action of photoreceptor proteins. The vitamin B12-dependent photoreceptor, CarH, is a bacterial transcriptional regulator that controls the biosynthesis of carotenoids to protect against photo-oxidative stress. The binding of B12 to CarH monomers in the dark results in the formation of a homo-tetramer that complexes with DNA; B12 photochemistry results in tetramer dissociation, releasing DNA for transcription. Although the details of the response of CarH to light are beginning to emerge, the biophysical mechanism of B12-binding in the dark and how this drives domain assembly is poorly understood. Here - using a combination of molecular dynamics simulations, native ion mobility mass spectrometry and time-resolved spectroscopy - we reveal a complex picture that varies depending on the availability of B12. When B12 is in excess, its binding drives structural changes in CarH monomers that result in the formation of head-to-tail dimers. The structural changes that accompany these steps mean that they are rate-limiting. The dimers then rapidly combine to form tetramers. Strikingly, when B12 is scarcer, as is likely in nature, tetramers with native-like structures can form without a B12 complement to each monomer, with only one apparently required per head-to-tail dimer. We thus show how a bulky chromophore such as B12 shapes protein/protein interactions and in turn function, and how a protein can adapt to a sub-optimal availability of resources. This nuanced picture should help guide the engineering of B12-dependent photoreceptors as light-activated tools for biomedical applications.

Experimental data on the effects that different antisolvents and antisolvent addition strategies have on nucleation behavior in antisolvent crystallization is very limited, and our understanding of these effects is sparse. In this work we measured the metastable zone width for the isothermal antisolvent crystallization of glycine from water utilizing methanol, ethanol, and dimethylformamide as antisolvents. We then investigated induction times for glycine crystallization across these metastable zones using the same three antisolvents. Supersaturated solutions were prepared by mixing of an antisolvent with undersaturated aqueous glycine solutions, either by batch rapid addition or using a continuous static mixer. Induction times were then recorded under agitated isothermal conditions in small vials with the use of webcam imaging and vary from apparently instant to thousands of seconds over a range of compositions and different mixing modes. Well-defined induction times were detected across most of the metastable zone, which shows that primary nucleation is significant at supersaturations much lower than those identified in conventional metastable zone width measurements. As supersaturation increases toward the metastable zone limit, crystal growth and secondary nucleation are likely to become rate-limiting factors in the observed induction times for antisolvent crystallization. Furthermore, the observed induction times were strongly dependent on the mode of mixing (batch rapid addition vs continuous static mixing), which demonstrates an interplay of antisolvent effects on nucleation with their effects on mixing, leading to crossover of mixing and nucleation time scales. This shows that appropriate mixing strategies are crucial for the rational development of robust scalable antisolvent crystallization processes.

In this chapter, we highlight recent developments using laser irradiation to probe ions in mass spectrometers. We will primarily cover the structural characterisation of biomolecules. This chapter will introduce the principles behind laser irradiation and describe some of the common instrument configurations, with an emphasis on benchtop laser systems coupled to instruments in laboratories. We have ordered the narrative in this chapter according to what has been achieved with three different irradiation wavelengths namely UV, visible and infrared. Instrumentation developed to permit laser irradiation along with mass spectrometry is described in each section along with some examples of recent applications primarily focused on the analysis of peptides and proteins.

The liquid-liquid transition in supercooled liquid water, predicted to occur around 220 K, is controversial due to the difficulty of studying it caused by competition from ice crystallization (the so-called "no man's land"). In aqueous solutions, it has been predicted to give rise to phase separation on a nanometer scale between a solute-rich high-density phase and a water-rich low-density phase. Here we report direct experimental evidence for the formation of a nanosegregated phase in eutectic aqueous solutions of LiCl and LiSCN where the presence of crystalline water can be experimentally excluded. Femtosecond infrared and Raman spectroscopies are used to determine the temperature-dependent structuring of water, the solvation of the SCN- anion, and the size of the phase segregated domains.

Ultrafast two-dimensional infrared (2D-IR) spectroscopy is a powerful probe of the structural and vibrational dynamics of proteins and enzymes in the solution phase. Until recently, relatively few applications of 2D-IR to DNA had been reported, but this is beginning to change rapidly, showing that the vibrational modes of DNA are sensitive reporters of base pairing and stacking and allowing site-specific probing of the nature of the complex interactions of the DNA macromolecule with its solvent environment. Most recently, 2D-IR spectroscopy has been used to probe the minor-groove ligand binding mechanism and reveals the melting of double-stranded DNA in real time, offering the potential for 2D-IR to provide mechanistic insight into the behavior of this most fundamental of biological molecules in the solution phase. The experimental methods used to obtain 2D-IR spectra are first described along with a discussion of the 2D-IR spectral features relevant to DNA studies before a review of the current state of the art of 2D-IR spectroscopy applications to DNA is presented.

The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced noncovalent interactions between the ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a suboptimal alternating A-T sequence. Results from two-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of the minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region. This induced fit maximizes favorable ligand-DNA enthalpic contributions in the optimal binding case and demonstrates that controlling the molecular details that induce subtle changes in DNA structure may hold the key to designing next-generation DNA-binding molecules.