Thermal Hazard Analysis of Two Non-Ideal Explosives Based on Ammonium Perchlorate/Ammonium Nitrate and Aluminium Powder.

In recent years, various kinds of civil explosive detonation accidents have occurred frequently around the world, resulting in substantial human casualties and significant property losses. It is generally believed that thermal stimulation plays a critical role in triggering the detonation of explosives; consequently, the study of the thermal hazards of explosives is of great significance to many aspects of safety emergency management practices in the production, transportation, storage, and use of explosives. It is known that the thermal stability of the ammonium perchlorate-aluminium system and the ammonium nitrate-aluminium system has been extensively investigated previously in the literature. However, there is a paucity of research on the thermal hazard characteristics of non-ideal explosives under varying oxygen balance conditions within the academic sphere. Therefore, this research focused on the study of the thermal hazards of non-ideal explosives based on thermokinetic analysis. The thermal hazards of non-ideal explosive mixtures of ammonium perchlorate and aluminium and of ammonium nitrate and aluminium were studied by thermal analysis kinetics. The thermokinetic parameters were meticulously studied through differential scanning calorimetry (DSC) analysis. The results showed that the peak reaction temperature and activation energy of the ammonium perchlorate-aluminium system were significantly higher than those of the ammonium nitrate-aluminium system. Under the condition of zero oxygen balance, the peak reaction temperature of the ammonium nitrate-aluminium system was 259 °C (heating rate 5 °C/min), and the activation energy was 84.7 kJ/mol. Under the same conditions, the peak reaction temperature and activation energy of the ammonium perchlorate-aluminium system were 292 °C (heating rate 5 °C/min) and 94.9 kJ/mol, respectively. These results indicate that the ammonium perchlorate-aluminium system has higher safety under the same thermal stimulation conditions. Furthermore, research on both non-ideal explosive systems reveals that the activation energy is at its peak under negative oxygen balance conditions, recorded at 104.2 kJ/mol (ammonium perchlorate-aluminium) and 86.2 kJ/mol (ammonium nitrate-aluminium), which indicates a higher degree of safety. Therefore, the investigation into the thermal hazards of non-ideal explosive systems under different oxygen balance conditions is of utmost importance for the enhancement and improvement of safety emergency management practices.

Difference in vaginal microecology, local immunity and HPV infection among childbearing-age women with different degrees of cervical lesions in Inner Mongolia.

BACKGROUND: This study aims to investigate the difference in vaginal microecology, local immunity and HPV infection among childbearing-age women with different degrees of cervical lesions. METHODS: A total of 432 patients were included in this study. Among these patients, 136 patients had LSIL, 263 patients had HSIL and 33 patients had CSCC. These patients were assigned as the research groups. In addition, 100 healthy females were enrolled and assigned as the control group. RESULTS: The microbiological indexes of vaginal secretions were evaluated. Furthermore, the concentrations of SIgA, IgG, IL-2 and IL-10 in vaginal lavage fluid, as well as the presence of HPV, mycoplasma and Chlamydia in cervical secretions, were detected. The results is that: (1) Differences in evaluation indexes of vaginal microecology among all research groups and the control group were statistically significant (P < 0.0001). As the degree of cervical lesions increased, the number of Lactobacillus decreased, and there was an increase in prevalence of bacterial imbalance, and the diversity, density and normal proportion of bacteria was reduced. Furthermore, the incidence of HPV, trichomonads, clue cell and Chlamydia infection increased. Moreover, the positive rate of H2O2 decreased, while the positive rates of SNa and GADP increased. (2) Differences in the ratio of IL-2 and IL-10 in the female genital tract among all research groups and the control group were statistically significant (P < 0.0001). CONCLUSIONS: As the degree of cervical lesions increased, IL-2 decreased, IL-10 increased and IL-2/IL-10 decreased, while SIgA and IgG were elevated. The reduction of dominant Lactobacillus in the vagina, impairment of H2O2 function, flora ratio imbalance, pathogen infections, reduction in IL-2/IL-10 ratio, and changes in SIgA and IgG levels could all be potential factors that influenced the pathogenicity of HPV infection and the occurrence and development of cervical lesions.

CaMKII Controls Whether Touch Is Painful.

The sensation of touch is initiated when fast conducting low-threshold mechanoreceptors (Aß-LTMRs) generate impulses at their terminals in the skin. Plasticity in this system is evident in the process of adaption, in which a period of diminished sensitivity follows prior stimulation. CaMKII is an ideal candidate for mediating activity-dependent plasticity in touch because it shifts into an enhanced activation state after neuronal depolarizations and can thereby reflect past firing history. Here we show that sensory neuron CaMKII autophosphorylation encodes the level of Aß-LTMR activity in rat models of sensory deprivation (whisker clipping, tail suspension, casting). Blockade of CaMKII signaling limits normal adaptation of action potential generation in Aß-LTMRs in excised skin. CaMKII activity is also required for natural filtering of impulse trains as they travel through the sensory neuron T-junction in the DRG. Blockade of CaMKII selectively in presynaptic Aß-LTMRs removes dorsal horn inhibition that otherwise prevents Aß-LTMR input from activating nociceptive lamina I neurons. Together, these consequences of reduced CaMKII function in Aß-LTMRs cause low-intensity mechanical stimulation to produce pain behavior. We conclude that, without normal sensory activity to maintain adequate levels of CaMKII function, the touch pathway shifts into a pain system. In the clinical setting, sensory disuse may be a critical factor that enhances and prolongs chronic pain initiated by other conditions. SIGNIFICANCE STATEMENT: The sensation of touch is served by specialized sensory neurons termed low-threshold mechanoreceptors (LTMRs). We examined the role of CaMKII in regulating the function of these neurons. Loss of CaMKII function, such as occurred in rats during sensory deprivation, elevated the generation and propagation of impulses by LTMRs, and altered the spinal cord circuitry in such a way that low-threshold mechanical stimuli produced pain behavior. Because limbs are protected from use during a painful condition, this sensitization of LTMRs may perpetuate pain and prevent functional rehabilitation.

Improving protein order-disorder classification using charge-hydropathy plots.

BACKGROUND: The earliest whole protein order/disorder predictor (Uversky et al., Proteins, 41: 415-427 (2000)), herein called the charge-hydropathy (C-H) plot, was originally developed using the Kyte-Doolittle (1982) hydropathy scale (Kyte & Doolittle., J. Mol. Biol, 157: 105-132(1982)). Here the goal is to determine whether the performance of the C-H plot in separating structured and disordered proteins can be improved by using an alternative hydropathy scale. RESULTS: Using the performance of the CH-plot as the metric, we compared 19 alternative hydropathy scales, with the finding that the Guy (1985) hydropathy scale (Guy, Biophys. J, 47:61-70(1985)) was the best of the tested hydropathy scales for separating large collections structured proteins and intrinsically disordered proteins (IDPs) on the C-H plot. Next, we developed a new scale, named IDP-Hydropathy, which further improves the discrimination between structured proteins and IDPs. Applying the C-H plot to a dataset containing 109 IDPs and 563 non-homologous fully structured proteins, the Kyte-Doolittle (1982) hydropathy scale, the Guy (1985) hydropathy scale, and the IDP-Hydropathy scale gave balanced two-state classification accuracies of 79%, 84%, and 90%, respectively, indicating a very substantial overall improvement is obtained by using different hydropathy scales. A correlation study shows that IDP-Hydropathy is strongly correlated with other hydropathy scales, thus suggesting that IDP-Hydropathy probably has only minor contributions from amino acid properties other than hydropathy. CONCLUSION: We suggest that IDP-Hydropathy would likely be the best scale to use for any type of algorithm developed to predict protein disorder.

Backbone Isomerization to Enhance Thermal Stability and Decrease Mechanical Sensitivities of 10 Nitro-Substituted Bipyrazoles.

The development of novel, environmentally friendly, and high-energy oxidizers remains interesting and challenging for replacing halogen-containing ammonium perchloride (AP). The trinitromethyl moiety is one of the most promising substituents for designing high-energy density oxidizers. In this study, a backbone isomerization strategy was utilized to manipulate the properties of 10 nitro group-substituted bipyrazoles containing the largest number of nitro groups among the bis-azole backbones so far. Another advanced high-energy density oxidizer, 3,3',5,5'-tetranitro-1,1'-bis(trinitromethyl)-1H,1'H-4,4'-bipyrazole (3), was designed and synthesized. Compared to the isomer 4,4',5,5'-tetranitro-2,2'-bis(trinitromethyl)-2H,2'H-3,3'-bipyrazole (4) (Td = 125 °C), 3 possesses better thermostability (Td = 156 °C), which is close to that of ammonium dinitramide (ADN) (Td = 159 °C), and it possesses better mechanical sensitivity (impact sensitivity (IS) = 13 J and friction sensitivity (FS) = 240 N) than that of 4 (IS = 9 J and FS = 215 N), thereby demonstrating a promising perspective for practical applications.

High-throughput characterization of intrinsic disorder in proteins from the Protein Structure Initiative.

The identification of intrinsically disordered proteins (IDPs) among the targets that fail to form satisfactory crystal structures in the Protein Structure Initiative represents a key to reducing the costs and time for determining three-dimensional structures of proteins. To help in this endeavor, several Protein Structure Initiative Centers were asked to send samples of both crystallizable proteins and proteins that failed to crystallize. The abundance of intrinsic disorder in these proteins was evaluated via computational analysis using predictors of natural disordered regions (PONDR®) and the potential cleavage sites and corresponding fragments were determined. Then, the target proteins were analyzed for intrinsic disorder by their resistance to limited proteolysis. The rates of tryptic digestion of sample target proteins were compared to those of lysozyme/myoglobin, apomyoglobin, and α-casein as standards of ordered, partially disordered and completely disordered proteins, respectively. At the next stage, the protein samples were subjected to both far-UV and near-UV circular dichroism (CD) analysis. For most of the samples, a good agreement between CD data, predictions of disorder and the rates of limited tryptic digestion was established. Further experimentation is being performed on a smaller subset of these samples in order to obtain more detailed information on the ordered/disordered nature of the proteins.

Molecular Dynamics Simulations of the Thermal Decomposition of 3,4-Bis(3-nitrofurazan-4-yl)furoxan.

When stimulated, for example, by a high temperature, the physical and chemical properties of energetic materials (EMs) may change, and, in turn, their overall performance is affected. Therefore, thermal stability is crucial for EMs, especially the thermal dynamic behavior. In the past decade, significant efforts have been made to study the thermal dynamic behavior of 3,4-bis(3-nitrofurazan-4-yl)furoxan (DNTF), one of the new high-energy-density materials (HEDMs). However, the thermal decomposition mechanism of DNTF is still not specific or comprehensive. In this study, the self-consistent-charge density-functional tight-binding method was combined with molecular dynamics (MD) simulations to reveal the differences in the thermal decomposition of DNTF under four heating conditions. The O-N (O) bond would fracture first during DNTF initial thermal decomposition at medium and low temperatures, thus triggering the cracking of the whole structure. At 2000 and 2500 K, NO2 loss on outer ring I is the fastest initial thermal decomposition pathway, and it determines that the decomposition mechanism is different from that of a medium-low temperature. NO2 is found to be the most active intermediate product; large molecular fragments, such as C2N2O, are found for the first time. Hopefully, these results could provide some insights into the decomposition mechanism of new HEDMs.

Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase.

The wide variety of protein structures and functions results from the diverse properties of the 20 canonical amino acids. The generally accepted hypothesis is that early protein evolution was associated with enrichment of a primordial alphabet, thereby enabling increased protein catalytic efficiencies and functional diversification. Aromatic amino acids were likely among the last additions to genetic code. The main objective of this study was to test whether enzyme catalysis can occur without the aromatic residues (aromatics) by studying the structure and function of dephospho-CoA kinase (DPCK) following aromatic residue depletion. We designed two variants of a putative DPCK from Aquifex aeolicus by substituting (a) Tyr, Phe and Trp or (b) all aromatics (including His). Their structural characterization indicates that substituting the aromatics does not markedly alter their secondary structures but does significantly loosen their side chain packing and increase their sizes. Both variants still possess ATPase activity, although with 150-300 times lower efficiency in comparison with the wild-type phosphotransferase activity. The transfer of the phosphate group to the dephospho-CoA substrate becomes heavily uncoupled and only the His-containing variant is still able to perform the phosphotransferase reaction. These data support the hypothesis that proteins in the early stages of life could support catalytic activities, albeit with low efficiencies. An observed significant contraction upon ligand binding is likely important for appropriate organization of the active site. Formation of firm hydrophobic cores, which enable the assembly of stably structured active sites, is suggested to provide a selective advantage for adding the aromatic residues.

The thermal decomposition process of Composition B by ReaxFF/lg force field.

Composition B is a melt-cast explosive consisting of mixtures of TNT and RDX. It has many excellent properties, but there are still multiple safety problems when it is used. Therefore, it is of importance to understand the thermal decomposition mechanism of Composition B. In this paper, during the establishment of the supercell model, the mass ratio of TNT to RDX is about 2:3, which accords with the actual proportion of formula of Composition B. Afterward, the thermal decomposition reaction of Composition B is conducted at various temperatures (2000 K, 2500 K, 3000 K, 3500 K, and 4000 K) by using molecular dynamics simulation of ReaxFF/lg. In terms of potential energy (PE) evolution, primary reaction, intermediate product, final product, and clusters, the thermal decomposition mechanism of Composition B is made an analysis. The activation energy of Composition B is 141.8 kJ/mol by fitting the kinetic parameters of the reaction. During the decomposition process of Composition B, the decay rate of RDX is faster than that of TNT, and the decay rates of TNT and RDX is accelerated significantly with the increasing temperature. The higher the temperature, the shorter the time difference between the two to fully decompose. It can be revealed from the result that the initial reaction path of Composition B decomposition is N-NO2 of RDX cleavage to form NO2, followed by the reaction of TNT with NO2 and other molecules. The initial decomposition reaction path of Composition B is the similar at different temperatures. The main products are small molecules (NO2, NO, N2O, H2O, CO2, N2, H2, HNO2, and HNO). Temperature can make a great difference for the structure of clusters. Large clusters in the system will break down into smaller molecules at high temperature.

--A high-throughput screen identifies inhibitors of the interaction between the oncogenic transcription factor ERG and the cofactor EWS.

Aberrant expression of the transcription factor ERG is a key driving event in approximately one-half of all of prostate cancers. Lacking an enzymatic pocket and mainly disordered, the structure of ERG is difficult to exploit for therapeutic design. We recently identified EWS as a specific interacting partner of ERG that is required for oncogenic function. In this study, we aimed to target this specific protein-protein interaction with small molecules. A high-throughput screening (HTS) strategy was implemented to identify potential protein-protein interaction inhibitors. Secondary assays verified the function of several hit compounds, and one lead compound inhibited ERG-mediated phenotypes in prostate cells. This is the first study aimed at targeting the ERG-EWS protein-protein interaction for the development of a small molecule-based prostate cancer therapy.

Many-to-one binding by intrinsically disordered protein regions.

Disordered binding regions (DBRs), which are embedded within intrinsically disordered proteins or regions (IDPs or IDRs), enable IDPs or IDRs to mediate multiple protein-protein interactions. DBR-protein complexes were collected from the Protein Data Bank for which two or more DBRs having different amino acid sequences bind to the same (100% sequence identical) globular protein partner, a type of interaction herein called many-to-one binding. Two distinct binding profiles were identified: independent and overlapping. For the overlapping binding profiles, the distinct DBRs interact by means of almost identical binding sites (herein called "similar"), or the binding sites contain both common and divergent interaction residues (herein called "intersecting"). Further analysis of the sequence and structural differences among these three groups indicate how IDP flexibility allows different segments to adjust to similar, intersecting, and independent binding pockets.

Association between interleukin-2, interleukin-10, secretory immunoglobulin A and immunoglobulin G expression in vaginal fluid and human papilloma virus outcome in patients with cervical lesions.

The present study was designed to investigate the association between a change in vaginal local immunity and human papilloma virus (HPV) infection outcome in patients with cervical lesions, through the study of the expression of vaginal local immune factors, interleukin (IL)-2, IL-10, secretory immunoglobulin A (sIgA) and IgG, in patients with different grades of cervical lesions and different degrees of cervical lesions caused by HPV infection prior to and following treatment. The experimental group comprised 136 patients with low-grade squamous intraepithelial lesions, 236 patients with high-grade squamous intraepithelial lesions and 133 patients with cervical squamous cell carcinoma, while the control group comprised 100 time- and location-matched healthy women. The concentrations of sIgA, IgG, IL-2 and IL-10 in the vaginal lavage fluid, were detected using ELISA prior to treatment and at 3, 6 and 12 months after treatment. Prior to treatment, differences in HPV infection rate and changes in vaginal immune factors between patients with all grades of lesions and controls were statistically significant (P<0.05). Furthermore, IL-2 and IL-10 expression levels and the IL-2/IL-10 ratio in patients with different grades of lesions, with or without seroconversion, were significantly different to those in controls (P<0.05). However, the differences between changes in IgG and sIgA expression between patients with HPV seroconversion and patients with persistent HPV infection were not statistically significant (P>0.05). The results of the present study suggest that the restoration of humoral immune function promotes HPV seroconversion, and that IL-2 and IL-10 levels and their ratio may reflect the severity of cervical lesions and treatment effects to a certain extent.

Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners.

BACKGROUND: Proteins are involved in many interactions with other proteins leading to networks that regulate and control a wide variety of physiological processes. Some of these proteins, called hub proteins or hubs, bind to many different protein partners. Protein intrinsic disorder, via diversity arising from structural plasticity or flexibility, provide a means for hubs to associate with many partners (Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN: Flexible Nets: The roles of intrinsic disorder in protein interaction networks. FEBS J 2005, 272:5129-5148). RESULTS: Here we present a detailed examination of two divergent examples: 1) p53, which uses different disordered regions to bind to different partners and which also has several individual disordered regions that each bind to multiple partners, and 2) 14-3-3, which is a structured protein that associates with many different intrinsically disordered partners. For both examples, three-dimensional structures of multiple complexes reveal that the flexibility and plasticity of intrinsically disordered protein regions as well as induced-fit changes in the structured regions are both important for binding diversity. CONCLUSIONS: These data support the conjecture that hub proteins often utilize intrinsic disorder to bind to multiple partners and provide detailed information about induced fit in structured regions.

The unfoldomics decade: an update on intrinsically disordered proteins.

BACKGROUND: Our first predictor of protein disorder was published just over a decade ago in the Proceedings of the IEEE International Conference on Neural Networks (Romero P, Obradovic Z, Kissinger C, Villafranca JE, Dunker AK (1997) Identifying disordered regions in proteins from amino acid sequence. Proceedings of the IEEE International Conference on Neural Networks, 1: 90-95). By now more than twenty other laboratory groups have joined the efforts to improve the prediction of protein disorder. While the various prediction methodologies used for protein intrinsic disorder resemble those methodologies used for secondary structure prediction, the two types of structures are entirely different. For example, the two structural classes have very different dynamic properties, with the irregular secondary structure class being much less mobile than the disorder class. The prediction of secondary structure has been useful. On the other hand, the prediction of intrinsic disorder has been revolutionary, leading to major modifications of the more than 100 year-old views relating protein structure and function. Experimentalists have been providing evidence over many decades that some proteins lack fixed structure or are disordered (or unfolded) under physiological conditions. In addition, experimentalists are also showing that, for many proteins, their functions depend on the unstructured rather than structured state; such results are in marked contrast to the greater than hundred year old views such as the lock and key hypothesis. Despite extensive data on many important examples, including disease-associated proteins, the importance of disorder for protein function has been largely ignored. Indeed, to our knowledge, current biochemistry books don't present even one acknowledged example of a disorder-dependent function, even though some reports of disorder-dependent functions are more than 50 years old. The results from genome-wide predictions of intrinsic disorder and the results from other bioinformatics studies of intrinsic disorder are demanding attention for these proteins. RESULTS: Disorder prediction has been important for showing that the relatively few experimentally characterized examples are members of a very large collection of related disordered proteins that are wide-spread over all three domains of life. Many significant biological functions are now known to depend directly on, or are importantly associated with, the unfolded or partially folded state. Here our goal is to review the key discoveries and to weave these discoveries together to support novel approaches for understanding sequence-function relationships. CONCLUSION: Intrinsically disordered protein is common across the three domains of life, but especially common among the eukaryotic proteomes. Signaling sequences and sites of posttranslational modifications are frequently, or very likely most often, located within regions of intrinsic disorder. Disorder-to-order transitions are coupled with the adoption of different structures with different partners. Also, the flexibility of intrinsic disorder helps different disordered regions to bind to a common binding site on a common partner. Such capacity for binding diversity plays important roles in both protein-protein interaction networks and likely also in gene regulation networks. Such disorder-based signaling is further modulated in multicellular eukaryotes by alternative splicing, for which such splicing events map to regions of disorder much more often than to regions of structure. Associating alternative splicing with disorder rather than structure alleviates theoretical and experimentally observed problems associated with the folding of different length, isomeric amino acid sequences. The combination of disorder and alternative splicing is proposed to provide a mechanism for easily "trying out" different signaling pathways, thereby providing the mechanism for generating signaling diversity and enabling the evolution of cell differentiation and multicellularity. Finally, several recent small molecules of interest as potential drugs have been shown to act by blocking protein-protein interactions based on intrinsic disorder of one of the partners. Study of these examples has led to a new approach for drug discovery, and bioinformatics analysis of the human proteome suggests that various disease-associated proteins are very rich in such disorder-based drug discovery targets.

TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorder.

Intrinsically disordered proteins carry out various biological functions while lacking ordered secondary and/or tertiary structure. In order to find general intrinsic properties of amino acid residues that are responsible for the absence of ordered structure in intrinsically disordered proteins we surveyed 517 amino acid scales. Each of these scales was taken as an independent attribute for the subsequent analysis. For a given attribute value X, which is averaged over a consecutive string of amino acids, and for a given data set having both ordered and disordered segments, the conditional probabilities P(s(o) | x) and P(s(d) | x) for order and disorder, respectively, can be determined for all possible values of X. Plots of the conditional probabilities P(s(o) | x) and P(s(o) | x) versus X give a pair of curves. The area between these two curves divided by the total area of the graph gives the area ratio value (ARV), which is proportional to the degree of separation of the two probability curves and, therefore, provides a measure of the given attribute's power to discriminate between order and disorder. As ARV falls between zero and one, larger ARV corresponds to the better discrimination between order and disorder. Starting from the scale with the highest ARV, we applied a simulated annealing procedure to search for alternative scale values and have managed to increase the ARV by more than 10%. The ranking of the amino acids in this new TOP-IDP scale is as follows (from order promoting to disorder promoting): W, F, Y, I, M, L, V, N, C, T, A, G, R, D, H, Q, K, S, E, P. A web-based server has been created to apply the TOP-IDP scale to predict intrinsically disordered proteins (http://www.disprot.org/dev/disindex.php).

Cardiac sodium channel palmitoylation regulates channel availability and myocyte excitability with implications for arrhythmia generation.

Cardiac voltage-gated sodium channels (Nav1.5) play an essential role in regulating cardiac electric activity by initiating and propagating action potentials in the heart. Altered Nav1.5 function is associated with multiple cardiac diseases including long-QT3 and Brugada syndrome. Here, we show that Nav1.5 is subject to palmitoylation, a reversible post-translational lipid modification. Palmitoylation increases channel availability and late sodium current activity, leading to enhanced cardiac excitability and prolonged action potential duration. In contrast, blocking palmitoylation increases closed-state channel inactivation and reduces myocyte excitability. We identify four cysteines as possible Nav1.5 palmitoylation substrates. A mutation of one of these is associated with cardiac arrhythmia (C981F), induces a significant enhancement of channel closed-state inactivation and ablates sensitivity to depalmitoylation. Our data indicate that alterations in palmitoylation can substantially control Nav1.5 function and cardiac excitability and this form of post-translational modification is likely an important contributor to acquired and congenital arrhythmias.

Small molecule activation of apurinic/apyrimidinic endonuclease 1 reduces DNA damage induced by cisplatin in cultured sensory neurons.

Although chemotherapy-induced peripheral neuropathy (CIPN) affects approximately 5-60% of cancer patients, there are currently no treatments available in part due to the fact that the underlying causes of CIPN are not well understood. One contributing factor in CIPN may be persistence of DNA lesions resulting from treatment with platinum-based agents such as cisplatin. In support of this hypothesis, overexpression of the base excision repair (BER) enzyme, apurinic/apyrimidinic endonuclease 1 (APE1), reduces DNA damage and protects cultured sensory neurons treated with cisplatin. Here, we address stimulation of APE1's endonuclease through a small molecule, nicorandil, as a means of mimicking the beneficial effects observed for overexpression of APE1. Nicorandil, was identified through high-throughput screening of small molecule libraries and found to stimulate APE1 endonuclease activity by increasing catalytic efficiency approximately 2-fold. This stimulation is primarily due to an increase in kcat. To prevent metabolism of nicorandil, an approved drug in Europe for the treatment of angina, cultured sensory neurons were pretreated with nicorandil and daidzin, an aldehyde dehydrogenase 2 inhibitor, resulting in decreased DNA damage but not altered transmitter release by cisplatin. This finding suggests that activation of APE1 by nicorandil in cisplatin-treated cultured sensory neurons does not imbalance the BER pathway in contrast to overexpression of the kinetically faster R177A APE1. Taken together, our results suggest that APE1 activators can be used to reduce DNA damage induced by cisplatin in cultured sensory neurons, although further studies will be required to fully assess their protective effects.

Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding.

Molecular recognition features (MoRFs) are intrinsically disordered protein regions that bind to partners via disorder-to-order transitions. In one-to-many binding, a single MoRF binds to two or more different partners individually. MoRF-based one-to-many protein-protein interaction (PPI) examples were collected from the Protein Data Bank, yielding 23 MoRFs bound to 2-9 partners, with all pairs of same-MoRF partners having less than 25% sequence identity. Of these, 8 MoRFs were bound to 2-9 partners having completely different folds, whereas 15 MoRFs were bound to 2-5 partners having the same folds but with low sequence identities. For both types of partner variation, backbone and side chain torsion angle rotations were used to bring about the conformational changes needed to enable close fits between a single MoRF and distinct partners. Alternative splicing events (ASEs) and posttranslational modifications (PTMs) were also found to contribute to distinct partner binding. Because ASEs and PTMs both commonly occur in disordered regions, and because both ASEs and PTMs are often tissue-specific, these data suggest that MoRFs, ASEs, and PTMs may collaborate to alter PPI networks in different cell types. These data enlarge the set of carefully studied MoRFs that use inherent flexibility and that also use ASE-based and/or PTM-based surface modifications to enable the same disordered segment to selectively associate with two or more partners. The small number of residues involved in MoRFs and in their modifications by ASEs or PTMs may simplify the evolvability of signaling network diversity.

Intrinsic protein disorder and protein-protein interactions.

Intrinsically disordered proteins often bind to more than one partner. In this study, we focused on 11 sets of complexes in which the same disordered segment becomes bound to two or more distinct partners. For this collection of protein complexes, two or more partners of each disordered segment were selected to have less than 25% amino acid identity at structurally aligned positions. As it turned out that most of the examples so selected had similar 3D structure, the studied set was reduced to just these similar-fold cases. Based on the analyses of the interacting partners, the average sequence identity of the partners' binding regions showed substantially higher conservation as compared to the nonbinding regions: The residue identities, averaged over the 11 sets of partner proteins, were as follows: binding residues, 42 ± 6%; nonbinding residues 20 ± 3%; nonbinding buried residues 26 ± 5%; and nonbinding surface residues 16 ± 3%. The higher sequence identity of the binding residues compared to the other sets of residues provides evidence that these observed interactions are likely to be meaningful biological interactions, not artifacts. Since many of the features of the various interactions indicate that the disordered binding segments were likely to have been disordered before binding, these results also add further weight to the existence and function of intrinsically disordered regions inside cells.