Structure, stability and folding of the alpha-helix

Pauling first described the alpha-helix nearly 50 years ago, yet new features of its structure continue to be discovered, using peptide model systems, site-directed mutagenesis, advances in theory, the expansion of the Protein Data Bank and new experimental techniques. Helical peptides in solution form a vast number of structures, including fully helical, fully coiled and partly helical. To interpret peptide results quantitatively it is essential to use a helix/coil model that includes the stabilities of all these conformations. Our models now include terms for helix interiors, capping, side-chain interactions, N-termini and 3(10)-helices. The first three amino acids in a helix (N1, N2 and N3) and the preceding N-cap are unique, as their amide NH groups do not participate in backbone hydrogen bonding. We surveyed their structures in proteins and measured their amino acid preferences. The results are predominantly rationalized by hydrogen bonding to the free NH groups. Stabilizing side-chain-side-chain energies, including hydrophobic interactions, hydrogen bonding and polar/non-polar interactions, were measured accurately in helical peptides. Helices in proteins show a preference for having approximately an integral number of turns so that their N- and C-caps lie on the same side. There are also strong periodic trends in the likelihood of terminating a helix with a Schellman or alpha L C-cap motif. The kinetics of alpha-helix folding have been studied with stopped-flow deep ultraviolet circular dichroism using synchrotron radiation as the light source; this gives a far superior signal-to-noise ratio than a conventional instrument. We find that poly(Glu), poly(Lys) and alanine-based peptides fold in milliseconds, with longer peptides showing a transient overshoot in helix content.     

Structure, expression, and heterogeneity of the rice seed prolamines

By screening two rice (Oryza sativa L.) seed cDNA libraries, recombinant cDNA clones encoding the rice prolamine seed storage protein were isolated. Based on cross-hybridization and restriction enzyme map analyses, these clones can be divided into two homology classes. All clones contain a single open reading frame encoding a putative rice prolamine precursor (molecular weight = 17,200) possessing a typical 14-amino acid signal peptide. The deduced primary structures of both types of prolamine polypeptides are devoid of repetitive sequences, a feature prevalent in other cereal prolamines. Clones of these two homology classes diverge mainly by insertions/deletions of short nucleotide stretches and point mutations. An isolated genomic clone about 15.5 kilobases in length displays a highly conserved 2.5-kilobase EcoRI fragment, repeated in tandem four times, each containing the prolamine coding sequence. Close homology is exhibited by the coding segments of the genomic and cDNA sequences, although the 5′ ends of the untranslated regions are widely divergent. The sequence heterogeneity displayed by these genomic and cDNA clones and large gene copy number (~80-100 copies/haploid genome) indicate that the rice prolamines are encoded by a complex multigene family.     

Structure, Dynamics, and Ion Conductance of the Phospholamban Pentamer

A 52-residue membrane protein, phospholamban (PLN) is an inhibitor of an adenosine-5′-triphosphate-driven calcium pump, the Ca²⁺-ATPase. Although the inhibition of Ca²⁺-ATPase involves PLN monomers, in a lipid bilayer membrane, PLN monomers form stable pentamers of unknown biological function. The recent NMR structure of a PLN pentamer depicts cytoplasmic helices extending normal to the bilayer in what is known as the bellflower conformation. The structure shows transmembrane helices forming a hydrophobic pore 4 Å in diameter, which is reminiscent of earlier reports of possible ion conductance through PLN pentamers. However, recent FRET measurements suggested an alternative structure for the PLN pentamer, known as the pinwheel model, which features a narrower transmembrane pore and cytoplasmic helices that lie against the bilayer. Here, we report on structural dynamics and conductance properties of the PLN pentamers from all-atom (AA) and coarse-grained (CG) molecular dynamics simulations. Our AA simulations of the bellflower model demonstrate that in a lipid bilayer membrane or a detergent micelle, the cytoplasmic helices undergo large structural fluctuations, whereas the transmembrane pore shrinks and becomes asymmetric. Similar asymmetry of the transmembrane region was observed in the AA simulations of the pinwheel model; the cytoplasmic helices remained in contact with the bilayer. Using the CG approach, structural dynamics of both models were investigated on a microsecond timescale. The cytoplasmic helices of the CG bellflower model were observed to fall against the bilayer, whereas in the CG pinwheel model the conformation of the cytoplasmic helices remained stable. Using steered molecular dynamics simulations, we investigated the feasibility of ion conductance through the pore of the bellflower model. The resulting approximate potentials of mean force indicate that the PLN pentamer is unlikely to function as an ion channel.     

Effect of Silicate Grain Shape, Structure, and Location on the Biomass and Community Structure of Colonizing Marine Microbiota

Microbiota colonizing silica grains of the same size and water pore space, but with a different microtopography, showed differences in biomass and community structure after 8 weeks of exposure to running seawater. The absence of surface cracks and crevices resulted in a marked diminution of the total microbial biomass measured as lipid phosphate and total extractable palmitic acid. With increasing smoothness of the sand grain surface, examination of the community structure showed a marked decrease in procaryotes and algal microeucaryotes, with a relative increase in microeucaryotic grazers. A comparison of the colonizing sediment incubated in running seawater or at 32 m on the sea floor with a sediment core showed a decreased bacterial biomass with a different community structure and a decreased total microeucaryotic population of both grazers and algae. The quantitative differences in microbial biomass and community structure between the microcosms and the actual benthic population in the core were determined.     

Structure, function and interactions of the PufX protein

The PufX protein is an important component of the reaction centre-light-harvesting 1 (RC-LH1) complex of Rhodobacter species of purple photosynthetic bacteria. Early studies showed that removal of the PufX protein causes changes in the structure of the RC-LH1 complex that result in a loss of the capacity for photosynthetic growth, and that this loss can be overcome though further mutations that change the structure of the LH1 antenna. More recent studies have examined interactions of the PufX protein with other components of the RC-LH1 complex. This review considers our current understanding of the structure and function of the PufX protein, how this protein interacts with other components of the photosynthetic membrane, and its influence on the oligomeric state of the RC-LH1 complex and the larger-scale architecture of the photosynthetic membrane.     

Structure, Function, and Evolution of Proton-ATPases

Proton-ATPases are among the most important primary ion pumps in nature. There are three classes of these enzymes which are distinguished by their structure, function, mechanism of action, and evolution. They function in ATP formation at the expense of a protonmotive force generated by oxidative and photosynthetic electron transports, maintaining a constant pH in the cytoplasm, and forming acidic spaces in special compartments inside and outside the cell. The three classes of proton-ATPases evolved in a way that prevents functional assembly in the wrong compartment. This was achieved by a triple genetic system located in the nucleus, mitochondria and chloroplast, as well as delicate control of the proton pumping activity of the enzymes.     

Structure,function, and regulation of thioesterases

Thioesterases are present in all living cells and perform a wide range of important biological functions by catalysing the cleavage of thioester bonds present in a diverse array of cellular substrates. Thioesterases are organised into 25 families based on their sequence conservation, tertiary and quaternary structure, active site configuration, and substrate specificity. Recent structural and functional characterisation of thioesterases has led to significant changes in our understanding of the regulatory mechanisms that govern enzyme activity and their respective cellular roles. The resulting dogma changes in thioesterase regulation include mechanistic insights into ATP and GDP-mediated regulation by oligomerisation, the role of new key regulatory regions, and new insights into a conserved quaternary structure within TE4 family members. Here we provide a current and comparative snapshot of our understanding of thioesterase structure, function, and regulation across the different thioesterase families.     

Gas Exchange of the Avian Egg Time, Structure, and Function

Data are presented for oxygen consumption water loss duringincubation water vapor conductance of the shell and pore numberof avian eggs and the way in which these values relate not onlyto egg mass but also to incubation time. It is proposed thatall these functions are proportional to the product of egg massand rate of development where the latter is defined as the inverseof incubation time. These interrelationships account at theend of incubation for similar O₂ and CO₂ tensions in the airspace of eggs utilization of calories (0.5 kcal g^–1) andwater loss (15 g g^–1)     

Structure,function, and evolution of the Orthobunyavirus membrane fusion glycoprotein

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Dynamics, Energetics, and Selectivity of the Low-K KcsA Channel Structure

Potassium channels are a diverse family of integral membrane proteins through which K⁺ can pass selectively. There is ongoing debate about the nature of conformational changes associated with the opening/closing and conductive/nonconductive states of potassium channels. The channels partly exert their function by varying their conductance through a mechanism known as C-type inactivation. Shortly after the activation of K⁺ channels, their selectivity filter stops conducting ions at a rate that depends on various stimuli. The molecular mechanism of C-type inactivation has not been fully understood yet. However, the X-ray structure of the KcsA channel obtained in the presence of low K⁺ concentration is thought to be representative of a K⁺ channel in the C-type inactivated state. Here, extensive, fully atomistic molecular dynamics and free-energy simulations of the low-K⁺ KcsA structure in an explicit lipid bilayer are performed to evaluate the stability of this structure and the selectivity of its binding sites. We find that the low-K⁺ KcsA structure is stable on the timescale of the molecular dynamics simulations performed, and that ions preferably remain in S1 and S4. In the absence of ions, the selectivity filter evolves toward an asymmetric architecture, as already observed in other computations of the high-K⁺ structure of KcsA and KirBac. The low-K⁺ KcsA structure is not permeable by Na⁺, K⁺, or Rb⁺, and the selectivity of its binding sites is different from that of the high-K⁺ structure.     

Structure, function, and long-term maintenance of the isolated turtle colon

We describe the 5-day maintenance of sacs of turtle colonic mucosa in enriched bathing solutions. The mean maximum transepithelial potential difference (PD) developed by the sacs in Ringer solution enriched with tissue-culture medium and gassed with 95% air-5% CO2 was 126 mV at 24 hours. Lower values were observed in other solutions. The PD of 24-hour sacs was partially or totally inhibited by ouabain, replacement of Na by choline in mucosal bathing fluids, or removal of Ca from serosal bathing fluids. The sacs transported Na in excess of H2O forming a dilute mucosal solution. The response of four different sac preparations (normally oriented or everted, and stripped normally oriented or everted) to long incubation were compared. Stripped normally oriented tissue developed the highest PD and maintained the lowest water content. The morphology of fresh and long-incubated tissue was examined. This investigation demonstrates that the turtle colon can be maintained in vitro for long periods, and it provides information on the morphology and physiology of this tissue.     

Structure, expression, and function of the Xenopus laevis caspase family

Caspases, a family of cysteine proteases, have been recognized as the central executors of programmed cell death. Nonetheless, the information on the caspase family has been limited to mammals, Drosophila, and nematodes. To examine the structure and characterization of the Xenopus caspase family, we have cloned the cDNAs encoding caspase-2 and -6-10 in addition to caspase-1 and -3, which we characterized previously (Yaoita, Y., and Nakajima, K. (1997) J. Biol. Chem. 272, 5122-5127). First, the existence of these caspases in frog suggests that the caspase cascades clarified in mammals are conserved at least from Amphibia. Interestingly, Xenopus caspase-1, -8, and -10 (especially caspase-8) showed a lower degree of identity to human equivalents than the other caspases. Second, mRNAs of many caspases increased during the climax of metamorphosis in regressing organs, tail, and intestine, where programmed cell death occurs, but not in apoptotic tail-derived cultured cells (XLT-15-11) treated with thyroid hormone, showing that new RNA synthesis of caspases is dispensable to programmed cell death. Third, comparison of human and Xenopus caspase sequences implies that some proposed regulations of human caspases are not conserved in frog.     

Evolutionary Epistemology, Social Epistemology, and the Demic Structure of Science

One of the principal difficulties in assessing Science as aProcess (Hull 1988) is determining the relationship between the various elements of Hull's theory. In particular, it is hard to understand precisely how conceptual selection is related to Hull's account of the social dynamics of science. This essay aims to clarify the relation between these aspects of his theory by examining his discussion of the``demic structure' of science. I conclude that the social account cando significant explanatory work independently of the selectionistaccount. Further, I maintain that Hull's treatment of the demicstructure of science points us toward an important set of issues insocial epistemology. If my reading of Science as a Process iscorrect, then most of Hull's critics (e.g., those who focus solelyon his account of conceptual selection) have ignored promisingaspects of his theory.     

Structure, isolation, composition and reconstitution of the neuronal fusion pore

Neuronal communication is dependent on the fusion of 40-50 nm in diameter synaptic vesicles containing neurotransmitters, at the presynaptic membrane. Here we report for the first time at 5-8A resolution, the presence of 8-10 nm in diameter cup-shaped neuronal fusion pores or porosomes at the presynaptic membrane, where synaptic vesicles dock and fuse to release neurotransmitters. The structure, isolation, composition, and functional reconstitution of porosomes present at the nerve terminal are described. These findings reveal the molecular mechanism of neurotransmitter release at the presynaptic membrane of nerve terminals.