Evolution of circular permutations in multidomain proteins

Modular rearrangements play an important role in protein evolution. Functional modules, often tantamount to structural domains or smaller fragments, are in many cases well conserved but reoccur in a different order and across many protein families. The underlying genetic mechanisms are gene duplication, fusion, and loss of sequence fragments. As a consequence, the sequential order of domains can be inverted, leading to what is known as circularly permutated proteins. Using a recently developed algorithm, we have identified a large number of such rearrangements and analyzed their evolutionary history. We searched for examples which have arisen by one of the three postulated mechanisms: independent fusion/fission, "duplication/deletion," and plasmid-mediated "cut and paste." We conclude that all three mechanisms can be observed, with the independent fusion/fission being the most frequent. This can be partly attributed to highly mobile domains. Duplication/deletion has been found in modular proteins such as peptide synthases.     

Rapid motif-based prediction of circular permutations in multi-domain proteins

MOTIVATION: Rearrangements of protein domains and motifs such as swaps and circular permutations (CPs) can produce erroneous results in searching sequence databases when using traditional methods based on linear sequence alignments. Circular permutations are also of biological relevance because they can help to better understand both protein evolution and functionality. RESULTS: We have developed an algorithm, RASPODOM, which is based on the classical recursive alignment scheme. Sequences are represented as strings of domains taken from precompiled resources of domain (motif) databases such as ProDom. The algorithm works several orders of magnitude faster than a reimplementation of the existing CP detection algorithm working on strings of amino acids, produces virtually no false positives and allows the discrimination of true CPs from 'intermediate' CPs (iCPs). Several true CPs which have not been reported in literature so far could be identified from Swiss-Prot/TrEMBL within minutes.     

Effect of circular permutations on transient partial unfolding in proteins

Under native conditions, proteins can undergo transient partial unfolding, which may cause proteins to misfold or aggregate. A change in sequence connectivity by circular permutation may affect the energetics of transient partial unfolding in proteins without altering the three‐dimensional structures. Using Escherichia coli dihydrofolate reductase (DHFR) as a model system, we investigated how circular permutation affects transient partial unfolding in proteins. We constructed three circular permutants, CP18, CP37, and CP87, with the new N‐termini at residue 18, 37, and 87, respectively, and probed transient partial unfolding by native‐state proteolysis. The new termini in CP18, CP37, and CP87 are within, near, and distal to the Met20 loop, which is known to be dynamic and also part of the region that undergoes transient unfolding in wild‐type DHFR. The stabilities of both native and partially unfolded forms of CP18 are similar to those of wild‐type DHFR, suggesting that the influence of introducing new termini in a dynamic region to the protein is minimal. CP37 has a significantly more accessible partially unfolded form than wild‐type DHFR, demonstrating that introducing new termini near a dynamic region may promote transient partial unfolding. CP87 has significantly destabilized native and partially unfolded forms, confirming that modification of the folded region in a partially unfolded form destabilizes the partially unfolded form similar to the native form. Our findings provide valuable guidelines to control transient partial unfolding in designing circular permutants in proteins.     

Deciphering the preference and predicting the viability of circular permutations in proteins

Circular permutation (CP) refers to situations in which the termini of a protein are relocated to other positions in the structure. CP occurs naturally and has been artificially created to study protein function, stability and folding. Recently CP is increasingly applied to engineer enzyme structure and function, and to create bifunctional fusion proteins unachievable by tandem fusion. CP is a complicated and expensive technique. An intrinsic difficulty in its application lies in the fact that not every position in a protein is amenable for creating a viable permutant. To examine the preferences of CP and develop CP viability prediction methods, we carried out comprehensive analyses of the sequence, structural, and dynamical properties of known CP sites using a variety of statistics and simulation methods, such as the bootstrap aggregating, permutation test and molecular dynamics simulations. CP particularly favors Gly, Pro, Asp and Asn. Positions preferred by CP lie within coils, loops, turns, and at residues that are exposed to solvent, weakly hydrogen-bonded, environmentally unpacked, or flexible. Disfavored positions include Cys, bulky hydrophobic residues, and residues located within helices or near the protein's core. These results fostered the development of an effective viable CP site prediction system, which combined four machine learning methods, e.g., artificial neural networks, the support vector machine, a random forest, and a hierarchical feature integration procedure developed in this work. As assessed by using the hydrofolate reductase dataset as the independent evaluation dataset, this prediction system achieved an AUC of 0.9. Large-scale predictions have been performed for nine thousand representative protein structures; several new potential applications of CP were thus identified. Many unreported preferences of CP are revealed in this study. The developed system is the best CP viability prediction method currently available. This work will facilitate the application of CP in research and biotechnology.     

Different circular permutations produced different folding nuclei in proteins: a computational study

There have been many studies about the effect of circular permutation on the transition state/folding nucleus of proteins, with sometimes conflicting conclusions from different proteins and permutations. To clarify this important issue, we have studied two circular permutations of a lattice protein model with side-chains. Both permuted sequences have essentially the same native state as the original (wild-type) sequence. Circular permutant 1 cuts at the folding nucleus of the wild-type sequence. As a result, the permutant has a drastically different nucleus and folds more slowly than wild-type. In contrast, circular permutant 2 involves an incision at a site unstructured in the wild-type transition state, and the wild-type nucleus is largely retained in the permutant. In addition, permutant 2 displays both two-state and multi-state folding, with a native-like intermediate state occasionally populated. Neither the wild-type nor permutant 1 has a similar intermediate, and both fold in an apparently two-state manner. Surprisingly, permutant 2 folds at a rate identical with that of the wild-type. The intermediate in permutant 2 is stabilised by native and non-native interactions, and cannot be classified simply as on or off-pathway. So we advise caution in attributing experimental data to on or off-pathway intermediates. Finally, our work illuminates the results on alpha-spectrin SH3, chymotrypsin inhibitor 2 and beta-lactoglobulin, and supports a key assumption in the experimental efforts to locate potential nucleation sites of real proteins via circular permutations.     

Naturally occurring erysipelas in rats

Erysipelothrix rhusiopathiae was isolated from the main limb joints of two Sprague Dawley rats affected by spontaneous lesions of chronic fibrinopurulent polyarthritis, endocarditis and mycocarditis.     

Naturally occurring triterpenoid saponins

Naturally occurring new triterpenoid saponins reported from mid-1996 to March, 2007 are reviewed including their physical constants and plant sources, and are compiled in Table 1. New saponins are arranged in Table 1 on the basis of the skeletal structures of their aglycones, e.g., oleanane type, ursane type, lupane type, hopane type, taraxastane type, cycloartane type, lanostane type, tirucallane type, dammarane type, cucurbitane type, and holostane type. The known triterpenoid saponins and prosapogenins of the new saponins, the biological and pharmacological activities of which were published during 1996-2007, are also reviewed together with their plant sources listed in Table 2 according to the skeletal structures of their aglycones in the same fashion as in Table 1. The plant and animal sources of both new and known bioactive triterpenoid saponins are collected in Table 3 in alphabetical order. The biological and pharmacological activities such as antiallergic, antiatherosclerosis and antiplatelet, antibacterial, anticomplementary, antidiabetic, contraceptive, antifungal, anti-inflammatory, antileishmanial, antimalarial/antiplasmodial, anti-obesity, anti-proliferative, antipsoriatic, antispasmodic, antisweet, antiviral, cytotoxic/antitumor, detoxication, gastroprotective, haemolytic, hepatoprotective, immunomodulatory, anti-enzyme, anti-osteoporotic, insecticidal, insulin-like, membrane-porosity, molluscicidal, neuropharmacological, anti-endothelial dysfunction, snake venom antidote, and sweet activities of these saponins or derived prosapogenins are discussed briefly after Table 3.     

Naturally occurring benzodiazepines in human milk

The presence of benzodiazepine-like molecules was detected radioimmunologically in the plasma and milk of 12 women and in the plasma of 9 men. All subjects were non-users of benzodiazepines. The concentration of these biological materials expressed as diazepam equivalents per mL amounted to 2.54 +/- 0.74 ng in male plasma; to 2.20 +/- 0.35 ng in female plasma and to 1.91 +/- 0.54 ng in milk. Further investigation of the active compounds in milk permitted the unequivocal identification of diazepam, both free and bound to a presumably protein carrier and, at least, three more benzodiazepine-like molecules. Their origin either from dietary sources or as a result of endogenous biosynthesis is still unclear.     

Naturally occurring genital mycoplasmosis in mice

The first isolations of Mycoplasma pulmonis were made from inflamed ovaries of 2 C3H/F1 mice. Investigation of cultures from a further 110 apparently healthy mice revealed 14 cases of M. pulmonis localized in the ovaries and associated with oophoritis.     

Naturally occurring Bacillus thuringiensis in Indonesia

S. HASTOWO, B.W. LAY AND M. OHBA. 1992. A total of 135 strains of Bacillus thuringiensis were isolated from soils of sericultural and natural environments of various regions in Indonesia: Sumatra, Java, Bali, Timor, Sulawesi and Kalimantan. Serologically, 63 strains were assigned to flagella (H) serotypes 3abc, 3ade, 4ac, 5ac, 6ab, 8ab, 9, 11, 17, 20ac, and 24, indicating a varied flora of B. thuringiensis in Indonesia. Of these, the serotype 3ade predominated, followed by the serotypes 3abc and 6ab. The other 72 strains (53·3%) were not sero-reactive against any of the H antisera to B. thuringiensis H serotypes 1–24. In toxicity tests, 34 strains belonging to serotypes 3abc, 3ade, 4ac, and 8ab showed larvicidal activity to the silkworm, Bombyx mori, while 74·8% did not exhibit insecticidal activity against larvae of B. mori and the mosquitoes, Aedes aegypti and Culex quinquefasciatus. Morphotypes of parasporal inclusions were not correlated with insecticidal activities.     

Naturally occurring hepatozoonosis in a coyote

Schizonts of Hepatozoon sp. were found in the myocardium of an adult cyote (Canis latrans) collected from the Aransas National Wildlife Refuge, Austwell, Texas. This constitutes the first time hepatozoonosis has been recorded in Canidae in the Western Hemisphere.     

Naturally occurring NAD-independent Haemophilus parainfluenzae

Four, NAD-independent, clinical isolates of Haemophilus parainfluenzae were recovered from a genital ulcer, a purulent skin lesion, a sputum specimen and a throat swab respectively. With the exception of NAD requirement, the strains exhibited the biochemical characteristics of H. parainfluenzae biotype II. The genetic relationship between these isolates and a standard strain of H. parainfluenzae was determined by testing transforming activities of two chromosomal markers, streptomycin resistance and nalidixic acid resistance. The clinical isolates were efficient donors and recipients in transformation. In addition, we demonstrated transfer of the genes conferring NAD independence to typical, NAD-requiring H. parainfluenzae and Haemophilus influenzae strains.