Engineering proteins with enhanced mechanical stability by force-specific sequence motifs

Use of atomic force microscopy (AFM) has recently led to a better understanding of the molecular mechanisms of the unfolding process by mechanical forces; however, the rational design of novel proteins with specific mechanical strength remains challenging. We have approached this problem from a new perspective that generates linear physical–chemical properties (PCP) motifs from a limited AFM data set. Guided by our linear sequence analysis, we designed and analyzed four new mutants of the titin I1 domain with the goal of increasing the domain's mechanical strength. All four mutants could be cloned and expressed as soluble proteins. AFM data indicate that at least two of the mutants have increased molecular mechanical strength. This observation suggests that the PCP method is useful to graft sequences specific for high mechanical stability to weak proteins to increase their mechanical stability, and represents an additional tool in the design of novel proteins besides steered molecular dynamics calculations, coarse grained simulations, and ?‐value analysis of the transition state. Proteins 2012; © 2011 Wiley Periodicals, Inc.     

Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method

The C-terminal domain (CTD) of the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (NP) contains a potential RNA-binding region in its N-terminal portion and also serves as a dimerization domain by forming a homodimer with a molecular mass of 28 kDa. So far, the structure determination of the SARS-CoV NP CTD in solution has been impeded by the poor quality of NMR spectra, especially for aromatic resonances. We have recently developed the stereo-array isotope labeling (SAIL) method to overcome the size problem of NMR structure determination by utilizing a protein exclusively composed of stereo- and regio-specifically isotope-labeled amino acids. Here, we employed the SAIL method to determine the high-quality solution structure of the SARS-CoV NP CTD by NMR. The SAIL protein yielded less crowded and better resolved spectra than uniform ¹³C and ¹⁵N labeling, and enabled the homodimeric solution structure of this protein to be determined. The NMR structure is almost identical with the previously solved crystal structure, except for a disordered putative RNA-binding domain at the N-terminus. Studies of the chemical shift perturbations caused by the binding of single-stranded DNA and mutational analyses have identified the disordered region at the N-termini as the prime site for nucleic acid binding. In addition, residues in the β-sheet region also showed significant perturbations. Mapping of the locations of these residues onto the helical model observed in the crystal revealed that these two regions are parts of the interior lining of the positively charged helical groove, supporting the hypothesis that the helical oligomer may form in solution.     

Competing phytoplankton undermines allelopathy of a bloom-forming dinoflagellate

Biotic interactions in the plankton can be both complex and dynamic. Competition among phytoplankton is often chemically mediated, but no studies have considered whether allelopathic compounds are modified by biotic interactions. Here, we show that compounds exuded during Karenia brevis blooms were allelopathic to the cosmopolitan diatom Skeletonema costatum, but that bloom allelopathy varied dramatically among collections and years. We investigated several possible causes of this variability and found that neither bloom density nor concentrations of water-borne brevetoxins correlated with allelopathic potency. However, when we directly tested whether the presence of competing phytoplankton influenced bloom allelopathy, we found that S. costatum reduced the growth-inhibiting effects of bloom exudates, suggesting that S. costatum has a mechanism for undermining K. brevis allelopathy. Additional laboratory experiments indicated that inducible changes to K. brevis allelopathy were restricted to two diatoms among five sensitive phytoplankton species, whereas five other species were constitutively resistant to K. brevis allelopathy. Our results suggest that competitors differ in their responses to phytoplankton allelopathy, with S. costatum exhibiting a previously undescribed method of resistance that may influence community structure and alter bloom dynamics.     

Direct action of endocrine disrupting chemicals on human sperm

Synthetic endocrine disrupting chemicals (EDCs), omnipresent in food, household, and personal care products, have been implicated in adverse trends in human reproduction, including infertility and increasing demand for assisted reproduction. Here, we study the action of 96 ubiquitous EDCs on human sperm. We show that structurally diverse EDCs activate the sperm‐specific CatSper channel and, thereby, evoke an intracellular Ca²⁺ increase, a motility response, and acrosomal exocytosis. Moreover, EDCs desensitize sperm for physiological CatSper ligands and cooperate in low‐dose mixtures to elevate Ca²⁺ levels in sperm. We conclude that EDCs interfere with various sperm functions and, thereby, might impair human fertilization.     

Random coil chemical shifts in acidic 8 M urea: Implementation of random coil shift data in NMRView

Studies of proteins unfolded in acid or chemical denaturant can help in unraveling events during the earliest phases of protein folding. In order for meaningful comparisons to be made of residual structure in unfolded states, it is necessary to use random coil chemical shifts that are valid for the experimental system under study. We present a set of random coil chemical shifts obtained for model peptides under experimental conditions used in studies of denatured proteins. This new set, together with previously published data sets, has been incorporated into a software interface for NMRView, allowing selection of the random coil data set that fits the experimental conditions best.     

Halting Regime Shifts in Floristically Intact Tropical Forests Deprived of Their Frugivores

Ecological restoration typically focuses on promoting vegetation recovery in degraded habitat or reintroducing endangered animals to enhance their regional or global persistence. Here, we argue that attention should also be devoted to vertebrate reintroductions in overhunted but floristically intact tropical forests in order to prevent insidious regime shifts in these systems. Growing evidence suggests that tropical forests deprived of seed‐dispersing animals exhibit replacement of fleshy fruiting trees by species with abiotic seed dispersal. Left unchecked, this process could eventually render the forest uninhabitable by frugivores through reduced density and diversity of their food plants. In tropical areas where hunting can be controlled, we contend that frugivore reintroduction, regulation of wild fruit harvest by humans, and outplanting of native fruiting trees should be deployed as management tools long before the systems are in need of traditional habitat restoration.     

Mapping of quantitative trait loci for clinical–chemical traits in swine

Clinical–chemical traits are diagnostic parameters essential for characterization of health and disease in veterinary practice. The traits show significant variability and are under genetic control, but little is known about the fundamental genetic architecture of this variability, especially in swine. We have identified QTL for alkaline phosphatase (ALP), lactate (LAC), bilirubin (BIL), creatinine (CRE) and ionized sodium (Na⁺), potassium (K⁺) and calcium (Ca⁺⁺) from the serum of 139 F₂ pigs from a Meishan/Pietrain family before and after challenge with Sarcocystis miescheriana , a protozoan parasite of muscle. After infection, the pigs passed through three stages representing acute disease, subclinical disease and chronic disease. Forty-two QTL influencing clinical–chemical traits during these different stages were identified on 15 chromosomes. Eleven of the QTL were significant on a genome-wide level; 31 QTL were chromosome-wide significant. QTL showed specific health/disease patterns with respect to the baseline values of the traits as well as the values obtained through the different stages of disease. QTL influencing different traits at different times were found primarily on chromosomes 1, 3, 7 and 14. The most prominent QTL for the investigated clinical–chemical traits mapped to SSC3 and 7. Baseline traits of ALP, LAC, BIL, Ca⁺⁺ and K⁺ were influenced by QTL regions on SSC3, 6, 7, 8 and 13. Single QTL explained up to 21.7% of F₂ phenotypic variance. Our analysis confirms that variation of clinical–chemical traits is associated with multiple chromosomal regions.     

Field Anesthesia and Health Assessment of Free-ranging <Emphasis Type="Italic">Cebus capucinus</Emphasis> in Panama

Health and disease are critical factors for understanding primate evolution and for developing effective conservation and management strategies. However, comprehensive health assessments of wild primate populations are rare, in part because of the difficulty and risk of chemically immobilizing subjects to obtain the necessary biological samples. We report here the results of a health assessment, as well as the methods and drug dosages used to capture white-faced capuchins (Cebus capucinus) on Barro Colorado Island, Panama. We captured and measured 24 capuchins as part of an ongoing radiotelemetry study, and collected biological samples from 9 of them for a comprehensive health survey. Telazol® was very effective for immobilizing and capturing capuchins, although the doses we used were higher than those recommended for captive capuchins. High Telazol doses immobilized individuals quickly, ensuring that we were able to find and recover the sedated monkeys. The capuchins were generally in good condition, and had few ecto-, hemo-, or intestinal parasites. However, all but 1 of the adults had substantial dental abnormalities. In addition, 1 juvenile had indeterminate genitalia that we believe to be the result of hypospadias. Seven of the capuchins tested positive for exposure to Herpesvirus tamarinus and all individuals tested positive for exposure to Cebus cytomegalovirus. Hematology, serum chemistry, and plasma mineral levels from the wild individuals were, for the most part, comparable to those recorded for captive Cebus capucinus, and contribute to establishing baseline health values for the species.     

药用柴胡属植物产地与化学成分相关性研究

从柴胡属植物品种入手,着重介绍药用柴胡属植物的生境分布、不同产地环境因子与柴胡化学成分研究进展,并为将来控制柴胡质量,解决柴胡资源有效途径提供方案.     

Analysis of essential histidine residues of maize branching enzymes by chemical modification and site-directed mutagenesis

Incubation of maize branching enzyme, mBEI and mBEII, with 100 μM diethylpyrocarbonate (DEPC) rapidly inactivated the enzymes. Treatment of the DEPC-inactivated enzymes with 100–500 mM hydroxylamine restored the enzyme activities. Spectroscopic data indicated that the inactivation of BE with DEPC was the result of histidine modification. The addition of the substrate amylose or amylopectin retarded the enzyme inactivation by DEPC, suggesting that the histidine residues are important for substrate binding. In maize BEII, conserved histidine residues are in catalytic regions 1 (His320) and 4 (His508). His320 and His508 were individually replaced by Ala via site-directed mutagenesis to probe their role in catalysis. Expression of these mutants inE. coli showed a significant decrease of the activity and the mutant enzymes hadK _m values 10 times higher than the wild type. Therefore, residues His320 and His508 do play an important role in substrate binding.