Lengths Of Helices Research Articles

Swellix: a computational tool to explore RNA conformational space

BackgroundThe sequence of nucleotides in an RNA determines the possible base pairs for an RNA fold and thus also determines the overall shape and function of an RNA. The Swellix program presented here combines a helix abstraction with a combinatorial approach to the RNA folding problem in order to compute all possible non-pseudoknotted RNA structures for RNA sequences. The Swellix program builds on the Crumple program and can include experimental constraints on global RNA structures such as the minimum number and lengths of helices from crystallography, cryoelectron microscopy, or in vivo crosslinking and chemical probing methods.ResultsThe conceptual advance in Swellix is to count helices and generate all possible combinations of helices rather than counting and combining base pairs. Swellix bundles similar helices and includes improvements in memory use and efficient parallelization. Biological applications of Swellix are demonstrated by computing the reduction in conformational space and entropy due to naturally modified nucleotides in tRNA sequences and by motif searches in Human Endogenous Retroviral (HERV) RNA sequences. The Swellix motif search reveals occurrences of protein and drug binding motifs in the HERV RNA ensemble that do not occur in minimum free energy or centroid predicted structures.ConclusionsSwellix presents significant improvements over Crumple in terms of efficiency and memory use. The efficient parallelization of Swellix enables the computation of sequences as long as 418 nucleotides with sufficient experimental constraints. Thus, Swellix provides a practical alternative to free energy minimization tools when multiple structures, kinetically determined structures, or complex RNA-RNA and RNA-protein interactions are present in an RNA folding problem.

Evolution and adaptation of single-pass transmembrane proteins

A comparative analysis of 6039 single-pass (bitopic) membrane proteins from six evolutionarily distant organisms was performed based on data from the Membranome database. The observed repertoire of bitopic proteins is significantly enlarged in eukaryotic cells and especially in multicellular organisms due to the diversification of enzymes, emergence of proteins involved in vesicular trafficking, and expansion of receptors, structural, and adhesion proteins. The majority of bitopic proteins in multicellular organisms are located in the plasma membrane (PM) and involved in cell communication. Bitopic proteins from different membranes significantly diverge in terms of their biological functions, size, topology, domain architecture, physical properties of transmembrane (TM) helices and propensity to form homodimers. Most proteins from eukaryotic PM and endoplasmic reticulum (ER) have the N-out topology. The predicted lengths of TM helices and hydrophobic thicknesses, stabilities and hydrophobicities of TM α-helices are the highest for proteins from eukaryotic PM, intermediate for proteins from prokaryotic cells, ER and Golgi apparatus, and lowest for proteins from mitochondria, chloroplasts, and peroxisomes. Tyr and Phe residues accumulate at the cytoplasmic leaflet of PM and at the outer leaflet of membranes of bacteria, Golgi apparatus, and nucleus. The propensity for dimerization increases from unicellular to multicellular eukaryotes, from enzymes to receptors, and from intracellular membrane proteins to PM proteins. More than half of PM proteins form homodimers with a 2:1 ratio of right-handed to left-handed helix packing arrangements. The inverse ratio (1:2) was observed for dimers from the ER, Golgi and vesicles.

Crumple: An Efficient Tool to Explore Thoroughly the RNA Folding Landscape.

The folding landscape for an RNA sequence contains many diverse structures and motifs, which are often sampled rather than completely explored. Today's supercomputers make the complete enumeration of all possible folds for an RNA and a detailed description of the RNA folding landscape a more feasible task. This chapter provides protocols for using the Crumple folding algorithm, an efficient tool to generate all possible non-pseudoknotted folds for an RNA sequence. Crumple in conjunction with Sliding Windows and Assembly can incorporate experimental constraints on the global features of an RNA, such as the minimum number and lengths of helices, which may be determined by crystallography or cryo-electron microscopy. This complete enumeration method is independent of free-energy minimization and allows the user to incorporate experimental data such as chemical probing, SELEX data on RNA-protein binding motifs, and phylogenetic covariation.

Crumple: A Method for Complete Enumeration of All Possible Pseudoknot-Free RNA Secondary Structures

The diverse landscape of RNA conformational space includes many canyons and crevices that are distant from the lowest minimum free energy valley and remain unexplored by traditional RNA structure prediction methods. A complete description of the entire RNA folding landscape can facilitate identification of biologically important conformations. The Crumple algorithm rapidly enumerates all possible non-pseudoknotted structures for an RNA sequence without consideration of thermodynamics while filtering the output with experimental data. The Crumple algorithm provides an alternative approach to traditional free energy minimization programs for RNA secondary structure prediction. A complete computation of all non-pseudoknotted secondary structures can reveal structures that would not be predicted by methods that sample the RNA folding landscape based on thermodynamic predictions. The free energy minimization approach is often successful but is limited by not considering RNA tertiary and protein interactions and the possibility that kinetics rather than thermodynamics determines the functional RNA fold. Efficient parallel computing and filters based on experimental data make practical the complete enumeration of all non-pseudoknotted structures. Efficient parallel computing for Crumple is implemented in a ring graph approach. Filters for experimental data include constraints from chemical probing of solvent accessibility, enzymatic cleavage of paired or unpaired nucleotides, phylogenetic covariation, and the minimum number and lengths of helices determined from crystallography or cryo-electron microscopy. The minimum number and length of helices has a significant effect on reducing conformational space. Pairing constraints reduce conformational space more than single nucleotide constraints. Examples with Alfalfa Mosaic Virus RNA and Trypanosome brucei guide RNA demonstrate the importance of evaluating all possible structures when pseduoknots, RNA-protein interactions, and metastable structures are important for biological function. Crumple software is freely available at http://adenosine.chem.ou.edu/software.html.

Essential Killing helices of order less than five on a non-flat complex space form

We study lengths of helices of orders 3 and 4 which are generated by some Killing vector fields on a complex projective plane and on a complex hyperbolic plane. We consider the moduli space of such helices under the congruence relation and give a lamination structure on this space which are closely related with the length spectrum. This shows that the moduli space does not form a canonical building structure with respect to the length spectrum.

Crystal Structure of the Ectodomain Complex of the CGRP Receptor, a Class-B GPCR, Reveals the Site of Drug Antagonism

Dysregulation of the calcitonin gene-related peptide (CGRP), a potent vasodilator, is directly implicated in the pathogenesis of migraine. CGRP binds to and signals through the CGRP receptor (CGRP-R), a heterodimer containing the calcitonin receptor-like receptor (CLR), a class B GPCR, and RAMP1, a receptor activity-modifying protein. We have solved the crystal structure of the CLR/RAMP1 N-terminal ectodomain heterodimer, revealing how RAMPs bind to and potentially modulate the activities of the CLR GPCR subfamily. We also report the structures of CLR/RAMP1 in complex with the clinical receptor antagonists olcegepant (BIBN4096BS) and telcagepant (MK0974). Both drugs act by blocking access to the peptide-binding cleft at the interface of CLR and RAMP1. These structures illustrate, for the first time, how small molecules bind to and modulate the activity of a class B GPCR, and highlight the challenges of designing potent receptor antagonists for the treatment of migraine and other class B GPCR-related diseases.

Predicting and Modeling RNA Architecture

A general approach for modeling the architecture of large and structured RNA molecules is described. The method exploits the modularity and the hierarchical folding of RNA architecture that is viewed as the assembly of preformed double-stranded helices defined by Watson-Crick base pairs and RNA modules maintained by non-Watson-Crick base pairs. Despite the extensive molecular neutrality observed in RNA structures, specificity in RNA folding is achieved through global constraints like lengths of helices, coaxiality of helical stacks, and structures adopted at the junctions of helices. The Assemble integrated suite of computer tools allows for sequence and structure analysis as well as interactive modeling by homology or ab initio assembly with possibilities for fitting within electronic density maps. The local key role of non-Watson-Crick pairs guides RNA architecture formation and offers metrics for assessing the accuracy of three-dimensional models in a more useful way than usual root mean square deviation (RMSD) values.

Clustering and Lateral Concentration of Raft Lipids by the MAL Protein

MAL, a compact hydrophobic, four-transmembrane-domain apical protein that copurifies with detergent-resistant membranes is obligatory for the machinery that sorts glycophosphatidylinositol (GPI)-anchored proteins and others to the apical membrane in epithelia. The mechanism of MAL function in lipid-raft-mediated apical sorting is unknown. We report that MAL clusters formed by two independent procedures-spontaneous clustering of MAL tagged with the tandem dimer DiHcRED (DiHcRED-MAL) in the plasma membrane of COS7 cells and antibody-mediated cross-linking of FLAG-tagged MAL-laterally concentrate markers of sphingolipid rafts and exclude a fluorescent analogue of phosphatidylethanolamine. Site-directed mutagenesis and bimolecular fluorescence complementation analysis demonstrate that MAL forms oligomers via xx intramembrane protein-protein binding motifs. Furthermore, results from membrane modulation by using exogenously added cholesterol or ceramides support the hypothesis that MAL-mediated association with raft lipids is driven at least in part by positive hydrophobic mismatch between the lengths of the transmembrane helices of MAL and membrane lipids. These data place MAL as a key component in the organization of membrane domains that could potentially serve as membrane sorting platforms.

Structure of the integral membrane domain of the GLP1 receptor

A three-dimensional (3D) model of the integral membrane domain of the GLP1 receptor, a member of the secretin receptor family of the G-protein-coupled receptor superfamily is proposed. The probable arrangement of the seven helices in this receptor was deduced from a detailed analysis of all the sequences in the secretin receptor family. The analysis includes: 1) identifying the transmembrane helices, 2) charge distribution analysis to estimate to which extent the transmembrane helices are buried, 3) Fourier transform analysis of different property profiles within the transmembrane helices to determine the orientation of exposed and buried faces of the helices, 4) alignment of sequences with those of the rhodopsin-like family using the novel "cold spot" method reported herein, 5) determination of lengths of transmembrane helices and their connecting loops and the constraints these impose on packing, tilting and organization, 6) incorporation of mutagenesis and ligand specificity data. We find that there is a close similarity between the structural properties of receptors of the secretin family and those of the rhodopsin-like family as typified by the frog rhodopsin structure recently solved by electron cryomicroscopy.

Binding Characteristics of Aromatase Inhibitors and Phytoestrogens to Human Aromatase

We have evaluated the binding characteristics of three steroidal inhibitors [4-hydroxyandrostene-dione (4-OHA), 7α-(4′-amino)phenylthio-1,4-androstadiene-3,17-dione (7α-APTADD), and bridge (2,19-methyleneoxy) androstene-3,17-dione (MDL 101,003)], four nonsteroidal inhibitors [aminoglutethimide (AG), CGS 20267, ICI D1033, and vorozole (R83842)], and two flavone phytoestrogens (chrysin, and 7,8-dihydroxyflavone) to aromatase through a combination of computer modeling and inhibitory profile studies on the wild-type and six aromatase mutants (I133Y, P308F, D309A, T310S, I395F, and I474Y). We have generated two aromatase models based on the x-ray structures of cytochrome P450-cam and cytochrome P450bm3, respectively. A major difference between the cytochrome P450cam-based and cytochrome P450bm3-based models is in the predicted lengths of helices F and G. In the cytochrome P450cam-based model, helices F and G lie antiparallel and extend across the active-site face of the molecule from one edge to the center, so that the carboxyl-terminal residues of helix F and the N-terminal residues of helix G make a major contribution to the structure of the active site. In the cytochrome P450bm3-based model, both helices are longer and so extend almost all the way across the active-site face of the molecule. Considering the size of the androgen substrate, we evaluated our results mainly based on the cytochrome P450cam model. The mutations involved in this study are thought to be at or near the proposed active site pocket. The inhibitory profile analysis has produced very interesting results and provided a molecular basis as to how seven aromatase inhibitors with different structures bind to the active site of aromatase. Furthermore, the investigation reveals that phytoestrogens bind to the active site of aromatase in a different orientation from that in the estrogen receptor.

Binding characteristics of aromatase inhibitors and phytoestrogens to human aromatase

We have evaluated the binding characteristics of three steroidal inhibitors [4-hydroxyandrostene-dione (4-OHA), 7α-(4′-amino)phenylthio-1,4-androstadiene-3,17-dione (7α-APTADD), and bridge (2,19-methyleneoxy) androstene-3,17-dione (MDL 101,003)], four nonsteroidal inhibitors [aminoglutethimide (AG), CGS 20267, ICI D1033, and vorozole (R83842)], and two flavone phytoestrogens (chrysin, and 7,8-dihydroxyflavone) to aromatase through a combination of computer modeling and inhibitory profile studies on the wild-type and six aromatase mutants (I133Y, P308F, D309A, T310S, I395F, and I474Y). We have generated two aromatase models based on the x-ray structures of cytochrome P450-cam and cytochrome P450bm3, respectively. A major difference between the cytochrome P450cam-based and cytochrome P450bm3-based models is in the predicted lengths of helices F and G. In the cytochrome P450cam-based model, helices F and G lie antiparallel and extend across the active-site face of the molecule from one edge to the center, so that the carboxyl-terminal residues of helix F and the N-terminal residues of helix G make a major contribution to the structure of the active site. In the cytochrome P450bm3-based model, both helices are longer and so extend almost all the way across the active-site face of the molecule. Considering the size of the androgen substrate, we evaluated our results mainly based on the cytochrome P450cam model. The mutations involved in this study are thought to be at or near the proposed active site pocket. The inhibitory profile analysis has produced very interesting results and provided a molecular basis as to how seven aromatase inhibitors with different structures bind to the active site of aromatase. Furthermore, the investigation reveals that phytoestrogens bind to the active site of aromatase in a different orientation from that in the estrogen receptor.

Structural studies on peptides corresponding to mutants of the major alpha-helix of barnase.

The structures of a family of peptides that contain variants of the major alpha-helix of barnase (residues 6-18) have been analyzed in solution by circular dichroism (CD) and 1H NMR at various concentrations of the helix-inducing cosolvent trifluoroethanol (TFE). The very low equilibrium constant (approximately 10(-2) for the formation of helix in water KH2O was estimated from titration of the helical ellipticity signal at 222 nm with [TFE] using the equation, KTFE = KH2O exp((m/RT) [TFE]/[H2O]), where KTFE is the equilibrium constant for the formation of helix in TFE/H2O and m is characteristic for each peptide but appears to be proportional to the lengths of related helices. NMR studies show that the peptide is mainly random coil in water, but that the helix is induced cooperatively by TFE and extends from residues 6 to 18 for wild-type peptide in 35% TFE. The mutant peptide Tyr-17-->Ala, however, has a helical region extending only for residues 9-15. Truncation of the helix upon mutation is also detected in the TFE titration procedure, which finds correspondingly lowered m-values upon mutation. This is is also supported by measurements of the pH dependence of KH2O, which is caused by the ionization of the C-cap residue, His-18, whose pKa is raised by the interaction of the protonated form with the helix dipole. Whereas there is an apparent charge/dipole interaction energy of 1.1 kcal mol-1 in the wild-type peptide, similar to that measured in the native protein, this drops dramatically upon mutations that disrupt the C-terminus of the helix. Mutation of Tyr-17-->Ala lowers KH2O only slightly, as do the other helix-destabilizing mutations. The combined results show that the helix-weakening effects of mutations act here primarily by shortening the length of the helix, with smaller effects on the equilibrium constants between helix and coil (KH2O).(ABSTRACT TRUNCATED AT 250 WORDS)

A model of morphogenesis for protein secondary structures

This paper proposes a model for the expected probability distribution for a certain class of biological structures. In particular, a model is derived for the distribution of lengths of helices, sheets, turns, and coils as a function of the length of the structure divided by the length of the protein it is contained in. A fit between the derived lognormal function and the structures for some proteins whose three-dimensional structure is known was significant. The fit produces fundamental parameters particular to each structure type that are related to the underlying structure and its morphogenesis. The importance of the result is that a universal mathematical distribution can be used to explain certain protein morphogeneses. Also, these fundamental parameters can be used as an aid in predicting whether a given sequence is a particular secondary structure or not, without a knowledge of its three-dimensional structure.

Membrane topography of ColE1 gene products: the hydrophobic anchor of the colicin E1 channel is a helical hairpin

The paucity of crystallographic data on the structure of intrinsic membrane proteins necessitates the development of additional techniques to probe their structures. The colicin E1 ion channel domain contains one prominent hydrophobic region near its COOH terminus that has been proposed to be an anchor for the assembly of the channel. Saturation site-directed mutagenesis of the hydrophobic anchor region of the colicin E1 ion channel was used to probe whether it spanned the bilayer once or twice. A nonpolar amino acid was replaced by a charged residue in 29 mutations made at 26 positions in the channel domain. Substitution of the charged amino acid at all positions except those in the center of the hydrophobic region and the periphery of the hydrophobic region caused a large decrease in the cytotoxicity of the purified mutant colicin E1 protein. This result implies that the hydrophobic domain spans the membrane bilayer twice in a helical hairpin loop, with the center of this domain residing in an aqueous or polar phase. The lengths of the trans-membrane helices appear to be approximately 18 and 16 residues. The absence of significant changes in ion selectivity in five of nine mutants indicated that these mutations did not cause a large change in the channel structure. The ion selectivity changes in four mutants and those previously documented for the flanking Lys residues imply that the hydrophobic hairpin is part of the channel lumen. Water may "abhor" the hydrophobic side of the channel, explaining the small effects of residue charge changes on ion selectivity.

The mould-filling capacity of two casting alloys

The mould-filling capacities of an Au-Ag-Cu alloy and a Ni-Cr-Be alloy for dental use have been studied by measuring the lengths of cast helices of a constant cross-section as a function of the supertemperature of the melt. A vacuum-pressure casting machine was applied in the experiments. Assuming that the conduction of heat through the investment is rate-controlling for the heat flow, the heat of fusion was calculated for the two alloys. These values were found to be close to those obtained by differential thermal analysis measurements. The lengths of the helices are strongly influenced by the deliberated heat of fusion during solidification. The substantially higher mould-filling capacity of the Ni-Cr-Be alloy compared with that of the Au-Ag-Cu alloy can be explained to a large extent by the corresponding difference in their latent heat of fusion. A calculation of the lengths of the helices requires a knowledge of the speeds of the melts. So far there are only indications of a higher speed for the Ni-Cr-Be alloy than for the Au-Ag-Cu alloy with the casting machine employed. The highest slope for the length of helix against supertemperature curve was observed for the Au-Ag-Cu alloy, indicating a smaller heat transfer coefficient for this alloy than for the Ni-Cr-Be alloy.

Chain flexibility and configurational dimensions of left handed Z- DNA and right handed B-DNA helices

The configurational behaviour of flexible helices of right handed B- and left handed Z-types have been analysed using statistical mechanical procedures. The configuration-dependent parameter, most importantly, the persistence length has been computed, using the heminucleotide scheme of treating polynucleotide chains under the approximation that perturbations in the backbone torsions produce sufficient flexibility in these helices. The values of persistence lengths obtained for Z-helices are very much higher than that of B-helices indicating that former is less flexible compared to the latter. These are in accordance with the results obtained recently on B- and Z-forms of poly(dG-dC). (dG-dC) using light scattering studies. Also the persistence lengths of BII-DNA helices characterised by a skew 3'-hemiucleotide (e-270°), and also when they coexist with B-DNA have been computed and the values lie within the range of experimentally reported values on B-helices. It is argued that the decrease in the persistence length values of B-DNA at higher salt concentration is due to additional small fluctuations in sugar residue torsions induced due to neutralisation of electrostatic repulsions between adjacent phosphates of the nucleotide. Noteworthy is that these are correlated to winding angle variations and the consequent bending of the helix.

Relationship between helix-coil transition parameters for synthetic polypeptides and helix conformation parameters for globular proteins. A simple model

o (1) The Zimm-Bragg formulation for helix-coil transitions in simple synthetic polypeptides is generalized to handle the formation of α-helical regions during the folding of globular proteins. (2) The relation between the helix-coil transition parameters for this process and other conformational parameters (derived by statistical analysis of the sequences and conformations of globular proteins_ is determined. (3) It is shown that the generalized Zimm-Bragg model can be used graphically to predict the helix-coil transition parameters from the statistical parameters, and vice versa . (4) It is also shown that the Zimm-Bragg co-operativity parameter σ implied by the lengths of helices observed in globular proteins is of the order of 10 −1 , and therefore much larger than the values obtained from simple synthetic polypeptides. (5) It is postulated that a similarly large value of σ persists throughout the folding process from the moment the helical regions are “trapped” by interactions between residues far apart in the amino acid sequence, and the nature of these interactions is discussed.

Studies on the secondary structure of ribosomal ribonucleic acid components of rabbit reticulocytes.

AbstractThe conformation in solution of fractionated 30 S and 19 S ribosomal RNA from rabbit reticulocytes has been studied by optical rotatory dispersion, analysis of thermal melting profiles and their derivatives, and spectrophotometric acid‐base titration. From a consideration of the limitations of these methods, it has been possible to set limiting values on the degree of base‐pairing and the lengths of the double helices: between 60 and 80% of the bases in 19 S and 30 S RNA are estimated to be paired. The paired segments are not shorter than 4 base pairs, and evidence from other sources is available which indicates that they are not longer than 8–16 base pairs. The spread of helix lengths is greater in the 30 S than in 19 S RNA; and other differences are noted. Several distinct populations of double helices, differing in their thermal stability, are present. Estimates are presented from spectrophotometric and titration data for the base compositions of the paired and unpaired regions.