New structures of allosteric proteins revealing remarkable conformational changes

New three-dimensional structures of allosteric proteins reveal they have a flexible architecture that is instrumental to the regulation of protein function. Highlights are the structures of GroEL, pyruvate kinase, -3-phosphoglycerate dehydrogenase and the acetylcholine receptor. Furthermore, significant progress in understanding the nature of the intermediates involved in an allosteric reaction has been achieved through recent spectroscopic and crystallographic studies on haemoglobin.     

Carbamoyl phosphate synthetase: a tunnel runs through it

The direct transfer of metabolites from one protein to another in a biochemical pathway or between one active site and another within a single enzyme has been described as substrate channeling. The first structural visualization of such a phenomenon was provided by the X-ray crystallographic analysis of tryptophan synthase, in which a tunnel of approximately 25 Å in length was observed. The recently determined three-dimensional structure of carbamoyl phosphate synthetase sets a new long distance record in that the three active sites are separated by nearly 100 Å.     

Permeability Changes of Manduca sexta Midgut Brush Border Membranes Induced by Oligomeric Structures of Different Cry Toxins

The pore-formation activity of monomeric and oligomeric forms of different Cry1 toxins (from Cry1A to Cry1G) was analyzed by monitoring ionic permeability across Manduca sexta brush border membrane vesicles. The membrane vesicles were isolated from microvilli structures, showing a high enrichment of apical membrane markers and low intrinsic K⁺ permeability. A fluorometric assay performed with 3,3′-dipropylthiodicarbocyanine fluorescent probe, sensitive to changes in membrane potential, was used. Previously, it was suggested that fluorescence determinations with this dye could be strongly influenced by the pH, osmolarity and ionic strength of the medium. Therefore, we evaluated these parameters in control experiments using the K⁺-selective ionophore valinomycin. We show here that under specific ionic conditions changes in fluorescence can be correlated with ionic permeability without effects on osmolarity or ionic strength of the medium. It is extremely important to attenuate the background response due to surface membrane potential and the participation of the endogenous permeability of the membrane vesicles. Under these conditions, we analyzed the pore-formation activity induced by monomeric and oligomeric structures of different Cry1 toxins. The Cry1 toxin samples containing oligomeric structures correlated with high pore activity, in contrast to monomeric samples that showed marginal pore-formation activity, supporting the hypothesis that oligomer formation is a necessary step in the mechanism of action of Cry toxins.     

The relationship between structure and function for the sulfite reductases

The six-electron reductions of sulfite to sulfide and nitrite to ammonia, fundamental to early and contemporary life, are catalyzed by diverse sulfite and nitrite reductases that share an unusual prosthetic assembly in their active centers, namely siroheme covalently linked to an Fe₄S₄ cluster. The recently determined crystallographic structure of the sulfite reductase hemoprotein from Escherichia coli complements extensive biochemical and spectroscopic studies in revealing structural features that are key for the catalytic mechanism and in suggesting a common symmetric structural unit for this diverse family of enzymes.     

GEFs, GAPs, GDIs and effectors: taking a closer (3D) look at the regulation of Ras-related GTP-binding proteins

Cell biology depends on the interactions of macromolecules, such as protein—DNA, protein—protein or protein—nucleotide interactions. GTP-binding proteins are no exception to the rule. They regulate cellular processes as diverse as protein biosynthesis and intracellular membrane trafficking. Recently, a large number of genes encoding GTP-binding proteins and the proteins that interact witht these molecular switches have been cloned and expressed. The 3D structures of some of these have also been elucidated     

Lipid polymorphism and biomembrane function

In recent years, several major developments have taken place in the biology, physical chemistry and technology of polymorphism of membrane lipids. These include the identification of polymorphic regulation of membrane lipid composition in Escherichia coli, the importance of nonbilayer lipids for protein functioning, the special packing properties of bilayers containing these lipids, and the crystalization of a membrane protein out of three dimensional bilayer networks (lipid cubic phases). These exciting developments bring us closer to understanding the paradox of the lipid bilayer structure of biomembranes and the molecular basis of membrane protein structure and function.     

RNA catalysis

Our understanding of the relationship between the structure of RNA and its catalytic activity has advanced significantly in the past year. These advances include time-resolved crystallographic studies on the hammerhead ribozyme, as well as new structures of a group I intron, a lead(II)-cleavage ribozyme, a hepatitis delta virus ribozyme, and components of the spliceosome machinery and the peptidyl transferase center of the ribosome and, most significantly, the structure of the ribosome itself.     

Structure and dynamics of green fluorescent protein

Many marine organisms are luminescent. The proteins that produce the light include a primary light producer (aequorin or luciferase) and often a secondary photoprotein that red shifts the light for better penetration in the ocean. Green fluorescent protein is one such secondary protein. It is remarkable in that it autocatalyzes the formation of its own fluorophore and thus can be expressed in variety of organisms in its fluorescent form. The recent determination of its 3D structure and other physical characterizations are revealing its molecular mechanism of action     

Structure of d-amino acid oxidase: new insights from an old enzyme

d-amino acid oxidase is the prototype of flavin-dependent oxidases. The recent resolution of its 3D structure has provided an explanation for several of its properties and has led to a substantial revision of the mechanism of d-amino acid dehydrogenation, with significant implications for the general uderstanding of flavin-dependent catalysis     

Differential requirement for the translocation of clostridial binary toxins: iota toxin requires a membrane potential gradient

Clostridial binary toxins, such as Clostridium perfringens Iota and Clostridium botulinum C2, are composed of a binding protein (Ib and C2-II, respectively) that recognizes distinct membrane receptors and mediates internalization of a catalytic protein (Ia and C2-I, respectively) with ADP-ribosyltransferase activity that depolymerizes the actin cytoskeleton. After internalization, it was found that C2 and Iota toxins were not routed to the Golgi apparatus and exhibited differential sensitivity to inhibitors of endosome acidification. While the C2-I component of C2 toxin was translocated into the cytosol from early endosomes, translocation of the Ia component of Iota toxin occurred between early and late endosomes, was dependent on more acidic conditions, and uniquely required a membrane potential gradient.     

Gen(om)e duplications in the evolution of early vertebrates

Phylogenetic analyses and sequence surveys of developmental regulator gene families indicate that two large-scale gene duplications, most likely genome duplications, occurred in ancestors of vertebrates. Relaxed constraints allowed duplicated and thus redundant genes to diverge in a two stage mechanism. Neutral changes dominated at first but then positively selected regulatory changes evolved the novel and increasingly complex vertebrate developmental program.     

Insights into the mechanisms of homologous recombination from the structure of RuvA

The recent structure determination of RuvA has provided the first insights into the structural basis for its interaction with Holliday junction DNA. Multiple copies of a helix-hairpin-helix motif which line the four grooves between the monomers in the tetrameric structure are thought to be involved in the interaction of the protein with its DNA target. This suggests that the four arms of the junction are held by RuvA in a fourfold symmetric arrangement and has fuelled ideas on the way in which components of the Ruv complex combine to catalyse the process of homologous recombination     

Chemical modification of Bacillus thuringiensis Cry1Aa toxin single-cysteine mutants reveals the importance of domain I structural elements in the mechanism of pore formation

Bacillus thuringiensis Cry toxins form pores in the apical membrane of insect larval midgut cells. To investigate their mechanism of membrane insertion, mutants in which cysteine replaced individual amino acids located within the pore-forming domain of Cry1Aa were chemically modified with sulfhydryl-specific reagents. The thiol group of cysteine was highly susceptible to oxidation and its reactivity was significantly increased when the toxins were purified under reducing conditions. Addition of a biotin group to the cysteine had little effect on the ability of the toxins to permeabilize Manduca sexta brush border membrane vesicles except for a slight reduction in activity for S252C and a large increase in activity for Y153C. The activity of Y153C was also significantly increased after modification by reagents that added an aromatic or a charged group to the cysteine. When permeability assays were performed in the presence of streptavidin, a large biotin-binding protein, the pore-forming activity of several mutants, including Y153C, where the altered residue is located within the hairpin comprising helices α4 and α5, or in adjacent loops, was significantly reduced. These results support the umbrella model of toxin insertion.     

The diversity of Bt resistance genes in species of Lepidoptera

Although the mode of action of Cry1A toxins produced by Bacillus thuringiensis is fairly well understood, knowledge of the molecular mechanisms by which lepidopteran species have evolved resistance to them is still in its infancy. The most common type of resistance has been called "Mode 1" and is characterized by recessive inheritance, >500-fold resistance to and reduced binding by at least one Cry1A toxin, and negligible cross-resistance to Cry1C. In three lepidopteran species, Heliothis virescens, Pectinophora gossypiella, and Helicoverpa armigera, Mode 1 resistance is caused by mutations in a toxin-binding 12-cadherin-domain protein expressed in the larval midgut. These mutations all interrupt the primary sequence of the protein and prevent its normal localization in the membrane, presumably removing a major toxic binding target of the Cry1A toxins. In Plutella xylostella, however, Mode 1 resistance appears to be caused by a different genetic mechanism, as Cry1A resistance is unlinked to the cadherin gene. Mapping studies in H. virescens have detected an additional major Cry1A resistance gene, which on the basis of comparative linkage mapping is distinct from the one in P. xylostella. An additional resistance mechanism supported by genetic data involves a protoxin-processing protease in Plodia interpunctella, and this is likely to be different from the genes mapped in Plutella and Heliothis. Thus, resistance to Cry1A toxins in species of Lepidoptera has a complex genetic basis, with at least four distinct, major resistance genes of which three are mapped in one or more species. The connection between resistance genes and the mechanisms they encode remains a challenging task to elucidate.     

Protein farnesyltransferase

In the past year, the crystal structure of αβ heterodimeric protein farnesyltransferase from rat was reported to a resolution of 2.25 Å. Farnesyltransferase catalyzes the essential post-transduction proteins. The structure provides a foundation for understanding the specificity and mechanism of protein prenylation and may aid in the design of new anticancer therapeutics.     

Solid-phase oligosaccharide synthesis and related technologies

Research efforts directed at the development of methodologies effective for solid-phase synthesis of oligosaccharides have resulted in a number of impressive achievements. In addition, closely related technologies, such as soluble polymer-supported synthesis and fluorous synthesis of the same class of molecules, have proved to be quite promising.     

Muscle proteins — their actions and interactions

Muscle contracts by the myosin cross-bridges ‘rowing’ the actin filaments past the myosin filaments. In the past year many structural details of this mechanism have become clear. Structural studies indicate distinct states for myosin S1 in the rigor, ATP or ‘down’ conformation and in the products complex (ADP·P_i) or ‘up’ state. Crystallographic studies substantiate this classification and yield details of the transformation. The isomerization ‘up’ to ‘down’ is the power stroke of muscle. This consists in the main of large changes of angle of the ‘lever arm’ (at the distal part of the myosin head) which can account for an 11 nm power stroke.     

Chain elongation in the isoprenoid biosynthetic pathway

Isoprenyl diphosphate synthases catalyze addition of allylic diphosphate primers to the isoprene unit in isopentenyl diphosphate to produce polyisoprenoid diphosphates with well defined chain lengths. Phylogenetic correlations suggest that the synthases which catalyze formation of isoprenoid diphosphates with (E) double bonds have evolved from a common ancestor. X-ray crystallographic studies of farnesyl diphosphate synthase in conjunction with site-directed mutagenesis have provided important new information about the residues involved in binding and catalysis and the source of chain length selectivity for the enzymes that catalyze chain elongation.     

About lipids and toxins

Many mono or multicellular organisms secrete soluble proteins, referred to as protein toxins, which alter the behavior of foreign, or target cells, possibly leading to their death. These toxins affect either the cell membrane by forming pores or modifying lipids, or some intracellular target. To reach this target, they must cross one of the cellular membranes, generally that of an intracellular organelle. As described in this minireview, lipids play crucial roles in the intoxication process of most if not all toxins, by allowing/promoting binding, endocytosis, trafficking and/or translocation into the cytoplasm.