From coarse-grain to all-atom: toward multiscale analysis of protein landscapes

Multiscale methods are becoming increasingly promising as a way to characterize the dynamics of large protein systems on biologically relevant time-scales. The underlying assumption in multiscale simulations is that it is possible to move reliably between different resolutions. We present a method that efficiently generates realistic all-atom protein structures starting from the C(alpha) atom positions, as obtained for instance from extensive coarse-grain simulations. The method, a reconstruction algorithm for coarse-grain structures (RACOGS), is validated by reconstructing ensembles of coarse-grain structures obtained during folding simulations of the proteins src-SH3 and S6. The results show that RACOGS consistently produces low energy, all-atom structures. A comparison of the free energy landscapes calculated using the coarse-grain structures versus the all-atom structures shows good correspondence and little distortion in the protein folding landscape.     

Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif

BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are dye-decolorizing peroxidases (DyPs), members of a new family of heme-dependent peroxidases recently identified in fungi and bacteria. Here, we report the crystal structures of BtDyP and TyrA at 1.6 and 2.7 A, respectively. BtDyP assembles into a hexamer, while TyrA assembles into a dimer; the dimerization interface is conserved between the two proteins. Each monomer exhibits a two-domain, alpha+beta ferredoxin-like fold. A site for heme binding was identified computationally, and modeling of a heme into the proposed active site allowed for identification of residues likely to be functionally important. Structural and sequence comparisons with other DyPs demonstrate a conservation of putative heme-binding residues, including an absolutely conserved histidine. Isothermal titration calorimetry experiments confirm heme binding, but with a stoichiometry of 0.3:1 (heme:protein).     

Alpha-methylation at benzylic fragment of N-aryl-N'-benzyl ureas provides TRPV1 antagonists with better pharmacokinetic properties and higher efficacy in inflammatory pain model

SAR studies for N-aryl-N'-benzyl urea class of TRPV1 antagonists have been extended to cover alpha-benzyl alkylation. Alkylated compounds showed weaker in vitro potencies in blocking capsaicin activation of TRPV1 receptor, but possessed improved pharmacokinetic properties. Further structural manipulations that included replacement of isoquinoline core with indazole and isolation of single enantiomer led to TRPV1 antagonists like (R)-16a with superior pharmacokinetic properties and greater potency in animal model of inflammatory pain.     

Resource-based adaptive divergence in the freshwater fish Telmatherina from Lake Matano, Indonesia

Adaptive radiations are an important source of biodiversity, but resolving which ecological pressures seed these processes in natural systems remains difficult. Here the adaptive radiation among Telmatherina, a genus of freshwater fish endemic to an ancient lake in central Sulawesi, Indonesia, was examined to determine its causal root. We demonstrate that all Telmatherina in this lake can be categorized into three lineages each possessing specialized skull shapes and pharyngeal jaw bones allowing them to exploit different resources. These data demonstrate a natural example of how resource partitioning has likely initiated adaptive radiation in a resource limited environment.     

The dynamics of signal triggering in a gp130-receptor complex

gp130 is a shared signal-transducing membrane-associated receptor for several hematopoietic cytokines. The 30 A resolution cryo-electron microscopy (cryo-EM) structure of the Interleukin 11(IL-11)-IL-11 Receptor-gp130 extracellular complex reveals the architecture and dynamics of this gp130-containing signaling complex. Normal-mode analysis reveals a repertoire of conformational changes that could function in signal triggering. This suggests a concerted mechanism of signaling involving all the components of the complex. This could provide a general mechanism of signal transfer for cytokines utilizing the JAK-STAT signaling cascade.     

Adaptation to culture of human embryonic stem cells and oncogenesis in vivo

The application of human embryonic stem cells (HESCs) to provide differentiated cells for regenerative medicine will require the continuous maintenance of the undifferentiated stem cells for long periods in culture. However, chromosomal stability during extended passaging cannot be guaranteed, as recent cytogenetic studies of HESCs have shown karyotypic aberrations. The observed karyotypic aberrations probably reflect the progressive adaptation of self-renewing cells to their culture conditions. Genetic change that increases the capacity of cells to proliferate has obvious parallels with malignant transformation, and we propose that the changes observed in HESCs in culture reflect tumorigenic events that occur in vivo, particularly in testicular germ cell tumors. Further supporting a link between culture adaptation and malignancy, we have observed the formation of a chromosomal homogeneous staining region in one HESC line, a genetic feature almost a hallmark of cancer cells. Identifying the genes critical for culture adaptation may thus reveal key players for both stem cell maintenance in vitro and germ cell tumorigenesis in vivo.     

Alterations of the biochemical pathways of plants by the air pollutant ozone: which are the true gauges of injury?

Plant strategies to survive ozone stress include exclusion or tolerance of ozone. If these processes fail, past observations of ozone injury have indicated many physiological and metabolic changes then occur; most of these changes are likely to have been initiated at the level of gene expression, suggesting signal transduction. In the last decade considerable understanding of the biochemical process within plants has been developed. Currently there are several hypotheses regarding a response of plants to ozone fumigation: [1] membrane dysfunction and alteration of purpose; [2] stress ethylene interactions; [3] impairment of photosynthesis via changes in Rubisco levels and the guard cells so that the stomata do not track correctly the environment; [4] antioxidant protection through metabolites and enzyme systems to reduce the oxidant load; and [5] general impairment or disruption of metabolic pathways. Many believe that free radicals and other oxidative products, formed in plant leaves under ozone exposure, are responsible for much of the spread of the biochemical alterations. There are obvious chemicals that may account for the changes that are observed, such as hydrogen peroxide. Once the ozone enters the tissue, evidence suggests the first line of defense is a range of antioxidants, such as ascorbate, glutathione peroxidase, superoxide dismutase, and catalase. If overwhelmed, subsequent events occur which are highly suggestive of systemic acquired resistance. Furthermore, other defensive indicators, such as salicylic acid and jasmonic acid, tend to increase, but more slowly than ethylene, and spread their signaling effects more widely in the plant. The primary set of metabolic reactions that ozone triggers is thought to be "wounding" responses with a secondary response of senescence. The dramatic strides in understanding the genetic make-up of plants, gene control, and signal transduction/control over the last few years will only accelerate in the future. We need now to have an understanding of those events that can be translated into more detailed schemes of how ozone alters much of the basic metabolism of plants and how plants counteract or cope with ozone. What is now known about how varied biochemicals and their pathways are changed upon ozone exposure will be discussed.     

Behavioral measurement of temperament in male nursery‐raised infant macaques and baboons

We define temperament as an individual's set of characteristic behavioral responses to novel or challenging stimuli. This study adapted a temperament scale used with rhesus macaques by Schneider and colleagues [American Journal of Primatology 25:137–155, 1991] for use with male pigtailed macaque (Macaca nemestrina, n = 7), longtailed macaque (M. Fascicularis, n = 3), and baboon infants (Papio cynocephalus anubis, n = 4). Subjects were evaluated twice weekly for the first 5 months of age during routine removal from their cages for weighing. Behavioral measures were based on the subject's interactions with a familiar human caretaker and included predominant state before capture, response to capture, contact latency, resistance to tester's hold, degree of clinging, attention to environment, defecation/urination, consolability, facial expression, vocalizations, and irritability. Species differences indicated that baboons were more active than macaques in establishing or terminating contact with the tester. Temperament scores decreased over time for the variables Response to Capture and Contact Latency, indicating that as they grew older, subjects became less reactive and more bold in their interactions with the tester. Temperament scores changed slowly with age, with greater change occurring at younger ages. The retention of variability in reactivity between and within species may be advantageous for primates, reflecting the flexibility necessary to survive in a changing environment. Am. J. Primatol. 47:43–50, 1999. © 1999 Wiley‐Liss, Inc.     

Dual cytoplasmic and nuclear distribution of the novel arsenite-stimulated human ATPase (hASNA-I)

The arsenite-stimulated human ATPase (hASNA-I) protein is a distinct human ATPase whose cDNA was cloned by sequence homology to the Escherichia coli ATPase arsA. Its subcellular localization in human malignant melanoma T289 cells was examined to gain insight into the role of hASNA-I in the physiology of human cells. Immunocytochemical staining using the specific anti-hASNA-I monoclonal antibody 5G8 showed a cytoplasmic, perinuclear, and nucleolar distribution. Subcellular fractionation indicated that the cytoplasmic hASNA-I was soluble and that the perinuclear distribution was due to association with the nuclear membrane rather than with the endoplasmic reticulum. Its presence in the nucleolus was confirmed by showing colocalization with an antibody of known nucleolar specificity. Further immunocytochemical analysis showed that the hASNA-I at the nuclear membrane was associated with invaginations into the nucleus in interphase cells. These results indicate that hASNA-I is a paralogue of the bacterial ArsA protein and suggest that it plays a role in the nucleocytoplasmic transport of a nucleolar component. J. Cell. Biochem. 71:1–10, 1998. © 1998 Wiley-Liss, Inc.     

Nitrogen-containing bisphosphonates as carbocation transition state analogs for isoprenoid biosynthesis.

Nitrogen-containing bisphosphonates are potent bone antiresorptive agents as well as having herbicidal and antiparasitic activity, and are thought to act by inhibiting enzymes of the mevalonate pathway. Using molecular modeling and ab initio quantum chemical calculations, we show that bisphosphonates can act as aza-isoprenoid transition state analogs, thereby inhibiting isoprenoid biosynthesis. The two phosphonate groups of the 1,1-bisphosphonates readily dock into the diphosphate-Mg(2+) binding site in farnesyl diphosphate synthase, while the charged ammonium (or pyridinium or imidazolium) groups act as carbocation transition state analogs, whose binding is stabilized by a cluster of oxygen atoms in the active site cleft, and an overall negative electrostatic potential in this region. Enhanced activity is shown to correlate with increasing van der Waals stabilization due to N-alkylation, or the presence of a charged, planar (sp(2)-hybridized) aromatic residue in the carbocation binding site. These results are of general interest since they suggest a rational approach to bisphosphonate drug design.