Hearts and Minds: Mental Health Support for schools

Hearts and Minds is a collection of generic mental health case studies written by students at the University of Southern Queensland. The mental health concerns focus on those typically experienced within schools and include Anxiety, Autism Spectrum Disorder, Attention Deficit Hyperactivity Disorder, Depression, Post-Traumatic Stress Disorder and Suicidal Ideation

Beyond the native state: Exploring the role of partially folded conformations on the protein energy landscape

Proteins can sample a variety of partially folded conformations during the transition between the unfolded and native states. The role of such intermediates is a matter of considerable debate, but it is clear that characterization of these partially folded species is crucial for understanding protein folding and function. A single amino acid change can convert E. coli ribonuclease H from a three-state folder that populates a kinetic intermediate to one that folds in an apparent two-state fashion. We have compared the folding trajectories of the three-state and two-state RNases H, proteins with the same native state topology but altered regional stability, using a protein engineering approach. Our data indicate that that both versions of RNase H fold through a similar trajectory with similar high-energy conformations. This suggests that formation of specific partially folded conformations may be a general feature of protein folding that can promote, rather than hinder, efficient folding.To better understand the robust role this high-energy species plays in folding, we set out to trap the transient intermediate of RNase H at equilibrium by selectively destabilizing the region of the protein known to be unfolded in this species. We find that the intermediate is undetectable in a series of HSQC's, revealing the dynamic nature of this partially folded form on the timescale of NMR detection. This result is in contrast to studies in which the structures of trapped intermediates are solved by NMR, indicating that the they are well-packed and native-like. The dynamic nature of the RNase H intermediate may be important for its role as an on-pathway, productive species that promotes efficient folding. An analogous intermediate is populated on the kinetic trajectory of RNase H from T. thermophilus, an organism that grows optimally at a temperature 30 oC higher than E. coli. To understand how two proteins that share identical structures can function in such different environments, we looked for differences in their energetics by comparing equilibrium mimics of their high-energy intermediates. We find potential differences in the dynamic properties of the intermediates, which may provide insight into how proteins with the same native structure can exhibit vastly different biophysical behavior.In contrast to globular proteins such as RNase H, repeat proteins are tandem arrays of repeating structural units that have no long-range contacts. In these modular domains, the majority of native contacts could be maintained in the face of partial unfolding. Repeat proteins therefore offer a unique architecture for exploring the extent of cooperativity and roughness on the energy landscape. To understand how a modular system builds cooperativity into its energetics, and to explore the origins and limits of this cooperativity, we studied the behavior of the Notch ankyrin domain in the optical tweezers, a single molecule mechanical tool. The forced unfolding of the Notch ankyrin domain occurs in one or two steps when manipulated in the optical tweezers. Though the unfolding pathway is heterogenous compared to that observed in bulk studies, there is a limit to the degree of uncoupling of individual repeats. We compare these results to the unfolding behavior of the Notch ankyrin domain in the atomic force microscope obtained by our collaborators for this project. This offers some insight into the apparent difference in solution and AFM unfolding of ankyrin repeat proteins

Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule

The molten globule, a conformational ensemble with significant secondary structure but only loosely packed tertiary structure, has been suggested to be a ubiquitous intermediate in protein folding. However, it is difficult to assess the tertiary packing of transiently populated species to evaluate this hypothesis. Escherichia coli RNase H is known to populate an intermediate before the rate-limiting barrier to folding that has long been thought to be a molten globule. We investigated this hypothesis by making mimics of the intermediate that are the ground-state conformation at equilibrium, using two approaches: a truncation to generate a fragment mimic of the intermediate, and selective destabilization of the native state using point mutations. Spectroscopic characterization and the response of the mimics to further mutation are consistent with studies on the transient kinetic intermediate, indicating that they model the early intermediate. Both mimics fold cooperatively and exhibit NMR spectra indicative of a closely packed conformation, in contrast to the hypothesis of molten tertiary packing. This result is important for understanding the nature of the subsequent rate-limiting barrier to folding and has implications for the assumption that many other proteins populate molten globule folding intermediates

Resonance Raman and UV-Vis Spectroscopic Characterization of FADH• in the Complex of Photolyase with UV-Damaged DNA

Escherichia coli photolyase uses blue light to repair cyclobutane pyrimidine dimers which are formed upon irradiation of DNA with ultraviolet (UV) light. E. coli photolyase is a flavoenzyme which contains a flavin adenine dinucleotide (FAD) in its active site and a 5,10-methenyltetrahydrofolate (MTHF) as a light-harvesting pigment. In the isolated enzyme, the FAD cofactor is present as a stable neutral radical semiquinone (FADH•). In this paper, we investigate the interaction between photolyase and UV-damage DNA by using resonance Raman and UV-vis spectroscopy. Substrate binding results in intensity changes and frequency shifts of the FADH• vibrations and also induces electrochromic shifts of the FADH• electronic transitions because of the substrate electric dipole moment. The intensity changes in the resonance Raman spectra can be largely explained by changes in the Raman excitation profiles because of the electrochromic shift. The size of the electrochromic shift suggests that the substrate binding geometry is similar to that of oxidized FAD in reconstituted photolyase. The frequency changes are partially a manifestation of the vibrational Stark effect induced by the substrate electric dipole moment but also because of small perturbations of the hydrogen-bonding environment of FADH• upon substrate binding. Furthermore, differences in the resonance Raman spectra of MTHF-containing photolyase and of an MTHF-less mutant suggests that MTHF may play a structural role in stabilizing the active site of photolyase while comparison to other flavoproteins indicates that the FAD cofactor has a strong hydrogen-bonding protein environment. Finally, we show that the electrochromic shift can be used as a direct method to measure photolyase-substrate binding kinetics

The Free Energy of Dissociation of Oligomeric Structure in Phycocyanin Is Not Linear with Denaturant

Using SEC HPLC and fluorescence anisotropy, absorption spectra were assigned to the specific oligomeric structures found with phycocyanin. The absorption spectra were used to quantify the population of each oligomeric form of the protein as a function of both urea concentration and temperature. Phycocyanin hexamers dissociate to trimers with equilibrium constants of 10 -6 to 10-5. Phycocyanin trimers dissociate to monomers with equilibrium constants of 10-15 to 10-12. Both dissociation constants increase linearly with increasing urea concentration, and ΔG° values calculated from the equilibrium constants fit best with an exponential function. Our findings appear in contrast with the commonly used linear extrapolation model, ΔGurea° = ΔG water° + A[denaturant], in which a linear relationship exists between the free energy of protein unfolding or loss of quaternary structure and the denaturant concentration. Our data examines a smaller range of denaturant concentration than generally used, which might partially explain the inconsistency

Identification of inactive conformation‐selective interleukin‐2‐inducible T‐cell kinase (ITK) inhibitors based on second‐harmonic generation

Many clinically approved protein kinase inhibitors stabilize an inactive conformation of their kinase target. Such inhibitors are generally highly selective compared to active conformation inhibitors, and consequently, general methods to identify inhibitors that stabilize an inactive conformation are much sought after. Here, we have applied a high‐throughput, second‐harmonic generation (SHG)‐based conformational approach to identify small molecule stabilizers of the inactive conformation of interleukin‐2‐inducible T‐cell kinase (ITK). A single‐site cysteine mutant of the ITK kinase domain was created, labeled with an SHG‐active dye, and tethered to a supported lipid bilayer membrane. Fourteen tool compounds, including stabilizers of the inactive and active conformations as well as nonbinders, were first examined for their effect on the conformation of the labeled ITK protein in the SHG assay. As a result, inactive conformation inhibitors were clearly distinguished from active conformation inhibitors by the intensity of SHG signal. Utilizing the SHG assay developed with the tool compounds described above, we identified the mechanism of action of 22 highly selective, inactive conformation inhibitors within a group of 105 small molecule inhibitors previously identified in a high‐throughput biochemical screen. We describe here the first use of SHG for identifying and classifying inhibitors that stabilize an inactive vs. an active conformation of a protein kinase, without the need to determine costructures by X‐ray crystallography. Our results suggest broad applicability to other proteins, particularly with single‐site labels reporting on specific protein movements associated with selectivity