Humanin is an endogenous human peptide with cytoprotective effects, including inhibition of apoptosis via interaction with BCL-2 proteins such as BAX. The therapeutic benefits of HN have been well-documented, and administering humanin and related endogenous human peptides for treatment of disease, aging, and enhancement of athletic performance is becoming more widespread. However, very little is known about the actual molecular structure of humanin and how it interacts with its protein partners. Here we present the amyloid-like β-sheet fibrillization of HN along with characterization of its secondary structure properties via transmission electron microscopy and other biophysical techniques. We identified several important HN mutants and documented their effects on the fibrillization process. Mutants that display inhibited β-sheet fibrillization were associated with those previously identified to be secretion deficient in vitro, highlighting the importance of β-sheet structure for membrane interactions. Successful β-sheet structural transitions are also required for productive interactions with BCL-2 family proteins resulting in apoptosis inhibition. Implications of fibrillization on the administration of HN is discussed.

Background Aneurysmal subarachnoid hemorrhage (aSAH) is a severe type of stroke that is associated with poor outcome. A subset of patients with aSAH will develop secondary complications, most notably delayed cerebral ischemia (DCI), which potentiates neurological injury. In this study, we investigate the relationship between cerebrospinal fluid (CSF) iron accumulation, brain metabolism, and neuronal injury in patients with aSAH with or without DCI. Methods We collected longitudinal CSF samples of patients immediately after hospitalization and 5 to 8 days after onset of ictus. CSF was analyzed with electron paramagnetic resonance spectroscopy and metabolomics to determine the presence of redox‐active iron species and metabolic alterations associated with aSAH and DCI. Neuronal pathology induced by iron overload was characterized in neuronal and meningeal cell models. Results Electron paramagnetic resonance spectroscopy identified higher levels of an Fe(III) protoporphyrin IX (hemin)‐like molecule in the CSF of patients who developed DCI compared with patients who did not show secondary ischemic injury after aSAH or controls without neurological disease. Treatment of a human neuronal cell line with Fe(III)‐containing hemin resulted in the disruption of the axonal mitochondrial network and loss of viability. This was cell‐type dependent as a meningeal cell line was resistant to hemin treatment, despite both cell types upregulating the iron ferroxidase ceruloplasmin. Metabolomic profiling of the same CSF samples uncovered significant dysregulation of metabolic pathways associated with energy generation and amino acid utilization, consistent with mitochondrial dysfunction. Using machine learning, we identified a set of metabolites that predicted intensive care unit length of stay. Conclusion aSAH leads to the accumulation of an Fe(III)‐containing heme species in the CSF of a subset of patients who subsequently develop DCI. The accumulation of an Fe(III) protoporphyrin induces axonal mitochondrial dysfunction, leading to cell death. aSAH alters the CSF metabolome involved in mitochondrial function and a subset of these metabolites are predictive of intensive care unit stay. These results identify potential biomarkers for mitochondrial pathology and provide insight into alterations in brain iron metabolism triggered by aSAH.

Autophagy allows cells to respond to acute stress or environmental change through the engulfment and degradation of cytoplasmic components. This can occur non-selectively in response to environmental changes or selectively via autophagic receptors to aid in quality control, maintenance, or immune functions. Initiation of autophagosome formation involves the Unc 51-like kinase 1 (ULK1) complex, comprised of ULK1 together with focal adhesion kinase family interacting protein of 200 kDa (FIP200) and the autophagy-related (ATG) proteins 101 and 13.

Commercial (protiated) samples of the "green" and biodegradable bioester 2-ethylhexyl laurate (2-EHL) were mixed with D-2-EHL synthesized by hydrothermal deuteration, with the mixtures demonstrating bulk structuring in small-angle neutron scattering measurements. Analysis in a polymer scattering framework yielded a radius of gyration (R (g)) of 6.5 angstrom and a Kuhn length (alternatively described as the persistence length or average segment length) of 11.2 angstrom. Samples of 2-EHL dispersed in acetonitrile formed self-assembled structures exceeding the molecular dimensions of the 2-EHL, with a mean aggregation number (N-agg) of 3.5 +/- 0.2 molecules across the tested concentrations. We therefore present structural evidence that this ester can function as a nonionic (co)-surfactant. The available surfactant-like conformations appear to enable performance beyond the low calculated hydrophilic-lipophilic balance value of 2.9. Overall, our data offer an explanation for 2-EHL's interfacial adsorption properties via self-assembly, resulting in strong emolliency and lubricity for this sustainable ester-based bio-oil.

Mitochondrial-derived peptides are encoded by mitochondrial DNA but have biological activity outside mitochondria. Eight of these are encoded by sequences within the mitochondrial 12S and 16S ribosomal genes: humanin, MOTS-c, and the six SHLP peptides, SHLP1-SHLP6. These peptides have various effects in cell culture and animal models, affecting neuroprotection, insulin sensitivity, and apoptosis, and some are secreted, potentially having extracellular signaling roles. However, except for humanin, their importance in normal cell function is unknown. To gauge their importance, their coding sequences in vertebrates have been analyzed for synonymous codon bias. Because they lie in RNA genes, such bias should only occur if their amino acids have been conserved to maintain biological function. Humanin and SHLP6 show strong synonymous codon bias and sequence conservation. In contrast, SHLP1, SHLP2, SHLP3, and SHLP5 show no significant bias and are poorly conserved. MOTS-c and SHLP4 also lack significant bias, but contain highly conserved N-terminal regions, and their biological importance cannot be ruled out. An additional potential mitochondrial-derived peptide sequence was discovered preceding SHLP2, named SHLP2b, which also contains a highly conserved N-terminal region with synonymous codon bias.

The self-diffusion coefficients of each of the components in mixtures containing pyridine and each of the homologous series 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imides in acetonitrile were determined using NMR diffusometry (i. e., Pulsed Gradient Spin Echo). The nature of solvation was found to change significantly with the proportion of salt in the mixtures. Increased diffusion coefficients (when corrected for viscosity) for the molecular components were observed with increasing proportion of ionic liquid and with increasing alkyl chain length on the cation. Comparison of the molecular solvents suggests increased interactions in solution of the pyridine with other components of the mixture, consistent with the proposed interactions shown previously to drive changes in reaction kinetics. Discontinuities were seen in the diffusion data for each species in solution across different ionic liquids between the hexyl and octyl derivatives, suggesting a change in the structuring in solution as the alkyl chain on the cation changes and demonstrating the importance of such when considering homologous series.

The varying conformational states of amyloid-forming protein monomers can determine their fibrillation outcome. In this study, we utilize solution NMR and the paramagnetic relaxation enhancement (PRE) effect to observe monomer properties of the repeat domain (RPT) from a human functional amyloid, premelanosomal protein, Pmel17. After excision from the full-length protein, RPT can self-assemble into amyloid fibrils, functioning as a scaffold for melanin deposition. Here, we report possible conformational states of the short RPT (sRPT) isoform, which has been demonstrated to be a fibrillation nucleator. NMR experiments were performed to determine conformational differences in sRPT by comparing aggregation-prone vs nonaggregating solution conditions. We observed significant chemical shift perturbations localized to residues near the C-terminus, demonstrating that the local chemical environment of the amyloid core region is highly sensitive to changes in pH. Next, we introduced cysteine point mutations for the covalent attachment of PRE ligands to sRPT to facilitate the observation of intramolecular interactions. We also utilized solvent PRE molecules with opposing charges to measure changes in the electrostatic potential of sRPT in different pH environments. These observed PRE effects offer insight into initial molecular events that might promote intermolecular interactions, which can trigger fibrillation. Taken together, our results show that sRPT monomers adopt a conformation inconsistent with a fully random coil at neutral pH and undergo conformational changes at lower pH values. These observations highlight regulatory mechanisms via organelle-associated pH conditions that can affect the fibrillation activity of proteins like RPT.

Abstract Mitochondrial-derived peptides are encoded by mitochondrial DNA but have biological activity outside mitochondria. Eight of these are encoded by sequences within the mitochondrial 12S and 16S ribosomal genes: humanin, MOTS-c, and the six SHLP peptides, SHLP1-SHLP6. These peptides have various effects in cell culture and animal models, affecting neuroprotection, insulin sensitivity, and apoptosis, and some are secreted, potentially having extracellular signaling roles. However, except for humanin, their importance in normal cell function is unknown. To gauge their importance, their coding sequences in vertebrates have been analyzed for synonymous codon bias. Because they lie in RNA genes, such bias should only occur if their amino acids have been conserved to maintain biological function. Humanin and SHLP6 show strong synonymous codon bias and sequence conservation. In contrast, SHLP1, SHLP2, SHLP3, and SHLP5 show no significant bias and are poorly conserved. MOTS-c, SHLP4 also lack significant bias, but contain highly conserved N-terminal regions, and their biological importance cannot be ruled out. An additional potential mitochondrial-derived peptide sequence was discovered preceding SHLP2, named SHLP2b, which also contains a highly conserved N-terminal region with synonymous codon bias.

In studying amyloid-forming proteins, it is imperative to determine the monomer conformational dynamics that precede fibrillation. This study utilizes NMR and the paramagnetic relaxation enhancement (PRE) effect to observe monomer properties of the repeat domain (RPT) from a human functional amyloid, premelanosomal protein (Pmel17). RPT is generated through Pmel17 post-translational processing during melanosome maturation. The melanosome is an acidic organelle within specialized cells where melanin biogenesis occurs. At low melanosomal pH, RPT self-assembles into amyloid fibrils, functioning as a scaffold for melanin deposition. Here, we report dynamics of the short (sRPT) isoform, which has been demonstrated to be a fibrillation nucleator. NMR experiments were performed to determine conformational differences in sRPT by comparing aggregation-prone vs. non-aggregating solution conditions at pH ranges from 4 to 6, respectively. We observed significant chemical shift perturbations localized to residues near the important singular tryptophan residue, demonstrating that the local chemical environment of the amyloid core region is sensitive to changes in pH even in the monomer form. Next, we introduced several cysteine point mutations in order to covalently attach PRE ligands to sRPT for observation of intramolecular interactions. Long-range PRE effects indicate potential contacts to residues on opposite ends of sRPT. These PRE effects might be an indication of initial molecular events to facilitate intermolecular interactions, which can go on to trigger fibrillation. These results also hint at a transient conformation that inhibits fibrillation. Thus, by raising or lowering solution pH, the relative population of this state would be modulated. Taken together, these results show that sRPT monomers adopt a conformation inconsistent with fully random coil at neutral pH and undergo conformational changes at lower pH values. These observations highlight the tight regulatory mechanisms that can affect fibrillation activity of proteins like RPT.

Glutaredoxins (GRXs) are a class of enzymes used in the reduction of protein thiols and the removal of reactive oxygen species. The CPYC active site of GRX is a plausible metal binding site, but was previously theorized not to bind metals due to its cis-proline configuration. We have shown that not only do several transition metals bind to the CPYC active site of the Brucella melitensis GRX but also report a model of a dimeric GRX in the presence of silver. This metal complex has also been characterized using enzymology, mass spectrometry, size exclusion chromatography, and molecular modeling. Metalation of GRX unwinds the end of the helix displaying the CPYC active site to accommodate dimerization in a way that is similar to iron sulfur cluster binding in related homologs and may imply that metal binding is a more common occurrence in this class of oxidoreductases than previously appreciated.

Neurodegenerative diseases often are associated with cellular dysregulation that results in premature cell death or apoptosis. A common example is the accumulation of amyloid plaques that promotes the excessive expression of p38 mitogen-activated protein kinase. The increased abundance of this enzyme leads to mass phosphorylation and activation of a protein from the B-cell lymphoma 2 (BCL-2) family, BAX. BAX is the central regulatory protein for mitochondrial outer membrane permeabilization (MOMP), a poration process that commits cells to apoptosis by releasing death-propagating factors from the mitochondria. Recent reports identify a naturally occurring peptide, Humanin (HN), that could block amyloid-beta-associated neuronal apoptosis by interacting with BCL-2 proteins. We recently showed humanin interaction leads to the amyloid-like fibrillation of BAX and a second BCL-2 family member, BID. We proposed this as a novel anti-apoptotic mechanism that inhibits pro-apoptotic BCL-2 proteins from initiating MOMP by sequestering them into fibrils, a heretofore unprecedented phenomenon that involves refolding globular BCL-2 proteins rapidly into fibrils where they undergo significant alpha-helix to beta-sheet fold-switching. Here we seek to further characterize the fibrillation and fold-switch in conditions that are known to induce amyloid fibrillation.

Neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's are associated with accumulation of amyloid plaques or amyloid‐like complexes that foster cellular dysregulation. For example, neurons with amyloid inclusions often undergo premature apoptosis resulting from excessive expression of p38 mitogen‐activated protein kinase. The increased abundance of this enzyme leads to mass phosphorylation and activation of a protein from the B‐cell lymphoma 2 (BCL‐2) family, BAX. BAX is the central regulatory protein for mitochondrial outer membrane permeabilization (MOMP), a poration process that commits cells to apoptosis by releasing death‐propagating factors from the mitochondria. Thus, it may be possible to prevent premature neuronal apoptosis by identifying endogenous factors that decrease the MOMP capacity of BAX and other pro‐apoptotic BCL‐2 proteins. Humanin (HN) is a mitochondria‐derived peptide that is released by the organelle in response to several stress stimuli. In the cytosol or on the mitochondrial membrane HN can counteract the death signal by forming specific complexes with some of the BCL‐2 proteins. We recently reported the in vitro amyloid‐like fibrillation of BAX and a second pro‐apoptotic family member, BID, with HN. We proposed this as a novel anti‐apoptotic mechanism that inhibits pro‐apoptotic BCL‐2 proteins from initiating MOMP by sequestering them into fibrils, a heretofore unprecedented phenomenon that involves refolding globular BCL‐2 proteins into fibrils where they undergo significant alpha‐helix to beta‐sheet fold‐switching. These fibrils represent a new direction for the field of cell death and elucidating mechanisms of the BCL‐2 family. The existence of this fold‐switching mechanism and fibrillation insists that at least some pro‐apoptotic members of the BCL‐2 family have unappreciated, functional beta‐sheet conformations. We hypothesize that in the membrane‐bound conformations these pro‐apoptotic BCL‐2 proteins might adopt beta‐sheet structures. Perhaps their fold‐switching dynamics may play a role in the pore‐forming process in the mitochondrial membrane, altering its membrane potential and leading up to the release of death factors into the cytosol. Therapeutics that can affect BCL‐2 protein propensity for either secondary structure state may prove to be fruitful toward ameliorating disease states where BCL‐2 family activity has become misregulated.

A series of ionic liquids based on the 1-alkyl-3-methylimidazolium cations were examined as components of the solvent mixture for a bimolecular substitution process. The effects on both the rate coefficient of the process and the NMR spin-spin relaxation of the solvent components of changing either the alkyl chain length or the amount of ionic liquid in the reaction mixture were determined. At a constant mole fraction, a shorter alkyl chain length resulted in a greater rate coefficient enhancement and a longer relaxation time, with the opposite effects for a longer alkyl chain length. For a given ionic liquid, increasing the proportion of salt in the reaction mixture resulted in a greater rate coefficient and a shorter relaxation time. The microscopic origins of the rate coefficient enhancement were determined and a step change found in the activation parameters on increasing the alkyl chain length from hexyl to octyl, suggesting notable structuring in solution. Across a range of ionic liquids and solvent compositions, the relaxation time from NMR measurements was shown to relate to the reaction rate coefficient. The approach of using fast and simple NMR relaxation measurements to predict reaction outcomes was exemplified using a morpholinium-based ionic liquid.

Members of the B-cell lymphoma (BCL-2) protein family regulate mitochondrial outer membrane permeabilization (MOMP), a phenomenon in which mitochondria become porous and release death-propagating complexes during the early stages of apoptosis. Pro-apoptotic BCL-2 proteins oligomerize at the mitochondrial outer membrane during MOMP, inducing pore formation. Of current interest are endogenous factors that can inhibit pro-apoptotic BCL-2 mitochondrial outer membrane translocation and oligomerization. A mitochondrial-derived peptide, Humanin (HN), was reported being expressed from an alternate ORF in the mitochondrial genome and inhibiting apoptosis through interactions with the pro-apoptotic BCL-2 proteins. Specifically, it is known to complex with BAX and BID. We recently reported the fibrillation of HN and BAX into β-sheets. Here, we detail the fibrillation between HN and BID. These fibers were characterized using several spectroscopic techniques, protease fragmentation with mass analysis, and EM. Enhanced fibrillation rates were detected with rising temperatures or pH values and the presence of a detergent. BID fibers are similar to those produced using BAX; however, the structures differ in final conformations of the BCL-2 proteins. BID fibers display both types of secondary structure in the fiber, whereas BAX was converted entirely to β-sheets. The data show that two distinct segments of BID are incorporated into the fiber structure, whereas other portions of BID remain solvent-exposed and retain helical structure. Similar analyses show that anti-apoptotic BCL-xL does not form fibers with humanin. These results support a general mechanism of sequestration of pro-apoptotic BCL-2 proteins into fibers by HN to inhibit MOMP.

Thermoresponsive polymers that display a lower critical solution temperature (LCST) are attractive drug delivery systems (DDSs) due to their potential to encapsulate and release therapeutics in a sustained manner as a function of temperature input. To attain the full potential of such DDSs, methods that illustrate the details of drug-polymer interactions are necessary. Here, we synthesized a nonionic, coacervate-forming, thermoresponsive polyester to encapsulate doxorubicin (Dox) and used solution state NMR spectroscopy and fluorescence microscopy techniques to probe the interactions between the polymer and Dox at the molecular level. The incomplete dehydration provides a matrix for encapsulation of sensitive therapeutics and preserving their activity, while the low hysteresis property of the polyester provides rapid transition from soluble to coacervate phase. Saturation transfer difference (STD) NMR revealed the Dox-polymer interactions within the coacervates. 1H-1H nuclear Overhauser effect spectroscopy (NOESY) cross-peak differences of Dox confirmed the Dox-polymer interactions. Diffusion-ordered spectroscopy (DOSY) revealed the slower diffusion rate of Dox in the presence of polyester coacervates. These studies illustrate how the state of the polyester (below and above LCST) affects the polyester-Dox interactions and offers details of the specific functional groups involved in these interactions. Our results provide a framework for future investigations aimed at characterizing fundamental interactions in polymer-based DDSs.

Rate constants for a bimolecular nucleophilic substitution (SN2) process in a range of ionic liquids are correlated with calculated parameters associated with the charge localisation on the cation of the ionic liquid (including the molecular electrostatic potential). Simple linear regression models proved effective, though the interdependency of the descriptors needs to be taken into account when considering generality. A series of ionic liquids were then prepared and evaluated as solvents for the same process; this data set was rationally chosen to incorporate homologous series (to evaluate systematic variation) and functionalities not available in the original data set. These new data were used to evaluate and refine the original models, which were expanded to include simple artificial neural networks. Along with showing the importance of an appropriate data set and the perils of overfitting, the work demonstrates that such models can be used to reliably predict ionic liquid solvent effects on an organic process, within the limits of the data set.