Minireview: structural insights into early folding events using continuous-flow time-resolved small-angle X-ray scattering

Small-angle X-ray scattering (SAXS) is a powerful method for obtaining quantitative structural information on the size and shape of proteins, and it is increasingly used in kinetic studies of folding and association reactions. In this minireview, we discuss recent developments in using SAXS to obtain structural information on the unfolded ensemble and early folding intermediates of proteins using continuous-flow mixing devices. Interfacing of these micromachined devices to SAXS beamlines has allowed access to the microsecond time regime. The experimental constraints in implementation of turbulence and laminar flow-based mixers with SAXS detection and a comparison of the two approaches are presented. Current improvements and future prospects of microsecond time-resolved SAXS and the synergy with ab initio structure prediction and molecular dynamics simulations are discussed.     

Insulin-like growth factor I receptor primary structure: comparison with insulin receptor suggests structural determinants that define functional specificity.

To identify structural characteristics of the closely related cell surface receptors for insulin and IGF-I that define their distinct physiological roles, we determined the complete primary structure of the human IGF-I receptor from cloned cDNA. The deduced sequence predicts a 1367 amino acid receptor precursor, including a 30-residue signal peptide, which is removed during translocation of the nascent polypeptide chain. The 1337 residue, unmodified proreceptor polypeptide has a predicted Mr of 151,869, which compares with the 180,000 Mr IGF-I receptor precursor. In analogy with the 152,784 Mr insulin receptor precursor, cleavage of the Arg-Lys-Arg-Arg sequence at position 707 of the IGF-I receptor precursor will generate alpha (80,423 Mr) and beta (70,866 Mr) subunits, which compare with approximately 135,000 Mr (alpha) and 90,000 Mr (beta) fully glycosylated subunits.     

Phosphorylation of tubulin and microtubule-associated proteins by the purified insulin receptor kinase

The purified insulin receptor kinase catalyzed the phosphorylation of native tubulin and microtubule-associated proteins (MAPs; MAP2, tau) on tyrosine residues. Insulin (10(-7) M) stimulated the reaction by 4-10-fold by increasing Vmax with little change in Km. alpha-Tubulin was preferred as a substrate for the kinase compared to beta-tubulin. MAP2 was found to be the best substrate among the cytoskeletal proteins tested; in the presence of insulin, the Vmax for MAP2 was 6.3 nmol/min/mg, its Km was 5.1 microM, and 1.7 mol of phosphate were incorporated per mol of MAP2. Under the same conditions used for this phosphorylation of tubulin and MAPs, actin and tropomyosin were very poorly phosphorylated. These data, coupled with previous evidence for potential functional relationships between insulin action and microtubules, raise the possibility that microtubule proteins may be cellular targets for the insulin receptor kinase.     

Evolution of style-length variability in figs and optimization of ovipositor length in their pollinator wasps: A coevolutionary model

Monoecious figs reward their pollinators—agaonid wasps—by allocating a proportion of the flowers for egg laying, and retain the rest for seed production. It has been suggested that these proportions could be regulated by producing short-styled and long-styled flowers such that pollinator wasps could only use the former as their ovipositor does not reach the ovules of the latter. Thus the wasps can lay eggs only in the short-styled flowers and raise their offspring, and the ovules of uninfested, long-styled flowers can develop into seeds. This implied that figs bear dimorphic female flowers, with a bimodal distribution of style length. However, recent studies have shown that style length is distributed normally, with no evidence of bimodality. Therefore the regulation of allocation of flowers to the wasps does not seem to be through the production of two distinct kinds of female flowers. In this article we suggest that two factors govern the proportion of flowers rewarded to the wasps: (i) passive regulation, which is a consequence of the optimization of wasp ovipositor length, and (ii) active regulation, where figs are selected to enhance the variance of style length. We show that these arguments lead to certain predictions about the optimum ovipositor length, the proportion of the flowers available to the wasps, and the coefficient of variation of style length. We also show that data for 18 fig-wasp associations conform well with these predictions. We finally suggest that the regulatory process outlined here can be extended to evolution of style length in dioecious fig species also.     

Intragenic duplication and divergence in the spectrin superfamily of proteins

Many structural, signaling, and adhesion molecules contain tandemly repeated amino acid motifs. The alpha-actinin/spectrin/dystrophin superfamily of F-actin-crosslinking proteins contains an array of triple alpha-helical motifs (spectrin repeats). We present here the complete sequence of the novel beta-spectrin isoform beta(Heavy)- spectrin (beta H). The sequence of beta H supports the origin of alpha- and beta-spectrins from a common ancestor, and we present a novel model for the origin of the spectrins from a homodimeric actin-crosslinking precursor. The pattern of similarity between the spectrin repeat units indicates that they have evolved by a series of nested, nonuniform duplications. Furthermore, the spectrins and dystrophins clearly have common ancestry, yet the repeat unit is of a different length in each family. Together, these observations suggest a dynamic period of increase in repeat number accompanied by homogenization within each array by concerted evolution. However, today, there is greater similarity of homologous repeats between species than there is across repeats within species, suggesting that concerted evolution ceased some time before the arthropod/vertebrate split. We propose a two-phase model for the evolution of the spectrin repeat arrays in which an initial phase of concerted evolution is subsequently retarded as each new protein becomes constrained to a specific length and the repeats diverge at the DNA level. This evolutionary model has general applicability to the origins of the many other proteins that have tandemly repeated motifs.      

Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae)

We examine rate heterogeneity among evolutionary lineages of the grass family at two plasmid loci, ndhF and rbcL, and we introduce a method to determine whether patterns of rate heterogeneity are correlated between loci. We show both that rates of synonymous evolution are heterogeneous among grass lineages and that are heterogeneity is correlated between loci at synonymous sites. At nonsynonymous sites, the pattern of rate heterogeneity is not correlated between loci, primarily due to an aberrant pattern of rate heterogeneity at nonsynonymous sites of rbcL. We compare patterns of synonymous rate heterogeneity to predictors based on the generation time effect and the speciation rate hypotheses. Although there is some evidence for generation time effects, neither generation time effects nor speciation rates appear to be sufficient to explain patterns of rate heterogeneity in the grass plastid sequences.      

Purification of insulin-like growth factor I receptor from human placental membranes

Insulin-like growth factor (IGF) I receptor was purified from Triton X-100-solubilized human placental membranes by wheat germ agglutinin-Sepharose chromatography followed by immunoaffinity chromatography using alpha IR-3, a monoclonal antibody directed against the IGF-I receptor. Purification of 3200-fold and 2800-fold was achieved from wheat germ agglutinin-Sepharose eluates with regard to IGF-I binding and kinase activities. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing conditions revealed two major protein bands corresponding to the alpha and beta subunits of the receptor, which accounted for at least 90% of the protein content. The purified receptor bound 10-20 micrograms of IGF-I/mg of protein and was more than 95% free of contamination by insulin receptor. It sedimented in glycerol gradients as a single species with a sedimentation coefficient of 13.7 S and gave three protein bands with Mr = approximately 300,000 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis under nonreducing conditions, indicating that alpha 2 beta 2 is an intact form of the IGF-I receptor. The purified receptor, when incubated with [gamma-32P] ATP, became phosphorylated at tyrosine residues of its beta subunit. This was stimulated 3-fold by IGF-I. It also had IGF-I-stimulated tyrosine kinase activity (5264 pmol of 32P incorporated/min/mg of protein) toward a synthetic peptide corresponding to the autophosphorylation site of pp60src. These data strongly suggest that it is a tyrosine-specific protein kinase.     

βα-Hairpin Clamps Brace βαβ Modules and Can Make Substantive Contributions to the Stability of TIM Barrel Proteins

Non-local hydrogen bonding interactions between main chain amide hydrogen atoms and polar side chain acceptors that bracket consecutive βα or αβ elements of secondary structure in αTS from E. coli, a TIM barrel protein, have previously been found to contribute 4–6 kcal mol⁻¹ to the stability of the native conformation. Experimental analysis of similar βα-hairpin clamps in a homologous pair of TIM barrel proteins of low sequence identity, IGPS from S. solfataricus and E. coli, reveals that this dramatic enhancement of stability is not unique to αTS. A survey of 71 TIM barrel proteins demonstrates a 4-fold symmetry for the placement of βα-hairpin clamps, bracing the fundamental βαβ building block and defining its register in the (βα)₈ motif. The preferred sequences and locations of βα-hairpin clamps will enhance structure prediction algorithms and provide a strategy for engineering stability in TIM barrel proteins.     

Transgenics of an elite <Emphasis Type="Italic">indica</Emphasis> rice variety Pusa Basmati 1 harbouring the <Emphasis Type="Italic">codA</Emphasis> gene are highly tolerant to salt stress

Transgenic lines of indica rice were generated by Agrobacterium-mediated transformation with the choline oxidase ( codA) gene from Arthrobacter globiformis. Choline oxidase catalyses conversion of choline to glycine betaine. Glycine betaine is known to provide tolerance against a variety of stresses. Molecular analyses of seven independent transgenic lines as performed by Southern, Northern and Western hybridization revealed integration and expression of the transgene as well as inheritance in the progeny plants. A good correlation was observed between levels of mRNA and protein accumulation, and a significant amount of choline oxidase product, i.e. glycine betaine, accumulated in R0 as well as R1 plants. Mendelian as well as non-Mendelian segregation patterns were obtained in the progeny plants. Challenge studies performed with R1 plants by exposure to salt stress (0.15 M NaCl) for 1 week, followed by a recovery period, revealed that in some cases more than 50% of the transgenic plants could survive salt stress and set seed whereas wild-type plants failed to recover.     

Prevalence of a calcium‐based alkaline phosphatase associated with the marine cyanobacterium Prochlorococcus and other ocean bacteria

Phosphate plays a key role in regulating primary productivity in several regions of the world's oceans and here dissolved organic phosphate can be an important phosphate source. A key enzyme for utilizing dissolved organic phosphate is alkaline phosphatase and the phoA‐type of this enzyme has a zinc cofactor. As the dissolved zinc concentration is low in phosphate depleted environments, this has led to the hypothesis that some phytoplankton may be zinc‐P co‐limited. Recently, it was shown that many marine bacteria contain an alternative form of alkaline phosphatase called phoX, but it is unclear which marine lineages carry this enzyme. Here, we describe the occurrence in low phosphate environments of phoX that is associated with uncultured Prochlorococcus and SAR11 cells. Through heterologous expression, we demonstrate that phoX encodes an active phosphatase with a calcium cofactor. The enzyme also functions with magnesium and copper, whereas cobalt, manganese, nickel and zinc inhibit enzyme activity to various degrees. We also find that uncultured SAR11 cells and cyanophages contain a different alkaline phosphatase related to a variant present in several Prochlorococcus isolates. Overall, the results suggest that many bacterial lineages including Prochlorococcus and SAR11 may not be subject to zinc‐P co‐limitation.