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Four coordination polymers have been synthesized by using Zn(II)/Cd(II) salt and bis(imidazole) ligand in the presence of the different flexible phenylenediacetate isomers under hydrothermal conditions. The flexible trans-conformation pda and biyb ligands in complexes 1, 3, 4 afford the 2D (4,4)-connected layer, which are further stacked in an offset fashion with an ABAB sequence to propagate into a 3D supramolecular architecture through strong C–H···π and C–H⋯O interactions. Differently, the flexible cis-conformation pda and biyb ligands in 2 can be seen as “V” type building block, linking Zn(II) atoms to form a 3D helix network. The structural diversity of these complexes is mainly attributed to the different coordination modes and isomer conformations of the flexible phenylenediacetic acids and bis(imidazole) ligand. The fluorescence property application and mechanisms of four complexes for detecting antibiotic cefixime (CEF) have been researched. Compared with 1, 3, 4 complex 2 has higher quenching percentage, this may be because 2 is a 3D structure with a large hole (18.99 × 20.02 A window). The detection limits of complexes 1–4 have been measured to be 0.23 μΜ, 0.34 μΜ, 0.37 μΜ, 0.38 μΜ, respectively. The theoretic calculation and UV–vis absorption experiments confirmed that the fluorescence quenching of complexes 1–4 toward cefixime (CEF) should be attributed to the electron transfer and the fluorescence inner filter effect between the fluorescent matter and the analyte.

Summary Recently identified proton-activated chloride channel (PAC) contains two transmembrane helices (S1–S2) and is involved in lysosome function, hypoxia adaption, stroke, and carcinogenesis. Although a PAC structure was recently resolved, its gating and activation mechanisms remained largely unknown. By the two-electrode voltage clamp electrophysiology in Xenopus oocytes, we found that the hydrophobicity of site 304 at fenestrations, but not that of neighbor sites, is important for maintaining PAC at a closed state at pH 7.5. When activated at acidic pH, PAC activity significantly increased with the hydrophilicity of site 307 within S2, but not with that of neighbor sites, suggesting that 307 acts as an activation gate. We identified six conserved protonatable residues critical for proton-induced activation, consistent with structural studies. Our study depicted a scheme in which proton binding induces conformational changes from the W304-controlled closed state at fenestrations to an activated state controlled by activation gate I307 in helix S2., Graphical abstract, Highlights • The hydrophobicity of site 304 is critical for maintaining PAC at a closed state • The function of activated PAC is modulated by the hydrophilicity of site 307 • Six protonatable amino acids are involved in proton-induced PAC activation • H+ binding seem to change PAC from W304-controlled closed to I307-gated open state, Molecular biology; Cell biology; Structural biology

We discuss linear and nonlinear topological edge states on the bearded-bearded edge (BBE) and armchair-armchair edge (AAE) of two helical waveguide arrays with opposite helicity. The robustness of the linear topological edge state can be controlled by the helix radius, the angle of the incidence, and the amplitude of lattice potentials. In the nonlinear regime, multipole-like lattice quasisolitons may be found with a certain saturable nonlinear factor for AAE. The long-distance propagation dynamics of such quasisolitons are numerically studied from the evolution of their intensity patterns and the “center of mass”. On the contrary, no quasisoltion exists for BBE under the same conditions.

The helical sense and elongation of a helical polymer that bears the 4-ethynylanilide of (R)-α‑methoxy-α-phenylacetic acid [m-(R)-1] can be tuned by the action of the two components of tetraalkylammonium-anion salts. Thus, while the supramolecular PPA-anilide/anion interaction creates a chiroptical switch, inducing either P or M helical senses in the poly(phenylacetylene) (PPA) depending on the nature of the anion —P helix: fluoride (F−) or cyanide (CN−); M helix: acetate (OAc−), benzoate (OBz−) or azide (N3−)—, deprotonation of the anilide group by these anions in dry conditions makes it possible to play with the elongation of the PPA, depending on the size of the tetraalkylammonium group, which results in a colorimetric switch. Thus, a color change from yellow to deep red is obtained by deprotonation of the anilide group when a tetraabutylammonium salt is used, while yellow/light-red and yellow/orange color changes are obtained when the size of the tetraalkylammonium group is reduced. Structural and mechanistic studies confirm that the color change occurs when the counterion accommodates itself close to the pendant group once the anilide hydrogen is removed. This PPA/tetraalkylammonium association is responsible of elongation changes in the PPA and therefore on the conjugation of the polyene backbone that is accompanied with color changes. Moreover, this colorimetric switch also operates in the solid state and can be switched in a vacuum/air moisture cycle Financial support from MINECO (PID2019-109733GB-I00), Xunta de Galicia (ED431C 2018/30; Centro singular de investigación de Galicia accreditation 2016–2019, ED431G/09 and the European Regional Development Fund (ERDF) is gratefully acknowledged. We also thank Servicio de Nanotecnología y Análisis de Superficies (CACTI, UVIGO) SI

Modulation of interactome networks, essentially protein-protein interactions (PPIs), might representvaluable therapeutic approaches to different pathological conditions. Since a high percentage of PPIs aremediated bya-helical structures at the interacting surface, the development of compounds able toreproduce the amino acid side-chain organization ofa-helices (e.g. stabilizeda-helix peptides andb-derivatives, proteomimetics, anda-helix small-molecule mimetics) focuses the attention of differentresearch groups. This appraisal describes the recent progress in the non-peptidea-helix mimeticsfield,which has evolved from single-face to multi-face reproducing compounds and from oligomeric tomonomeric scaffolds able to bear different substituents in similar spatial dispositions as the side-chainsin canonical helices. Grouped by chemical structures, the review contemplates terphenyl-like molecules,oligobenzamides and heterocyclic analogues, benzamide-amino acid conjugates and non-oligomericsmall-molecules mimetics, among others, and their effectiveness to stabilize/disrupt therapeuticallyrelevant PPIs. The X-ray structures of a couple of oligomeric peptidomimetics and of some small-molecules complexed with the MDM2 protein, as well as the state of the art on their development inclinical trials, are also remarked. The discovery of a continuously increasing number of new disease-relevant PPIs could offer future opportunities for these and other forthcominga-helix mimetics., This research was funded by grants from the Spanish Ministerio de Ciencia, Innovación y Universidades (MICIU-FEDER), grantnumber RTI2018-097189-B-C22 to RGM, and CSIC grant numbers201880E109 to MMM and 2019E030 to RGM.

Class I terpene synthase (TPS) generates bioactive terpenoids with diverse backbones. Sesterterpene synthase (sester-TPS, C25), a branch of class I TPSs, was recently identified in Brassicaceae. However, the catalytic mechanisms of sester-TPSs are not fully understood. Here, we first identified three nonclustered functional sester-TPSs (AtTPS06, AtTPS22, and AtTPS29) in Arabidopsis thaliana. AtTPS06 utilizes a type-B cyclization mechanism, whereas most other sester-TPSs produce various sesterterpene backbones via a type-A cyclization mechanism. We then determined the crystal structure of the AtTPS18–FSPP complex to explore the cyclization mechanism of plant sester-TPSs. We used structural comparisons and site-directed mutagenesis to further elucidate the mechanism: (1) mainly due to the outward shift of helix G, plant sester-TPSs have a larger catalytic pocket than do mono-, sesqui-, and di-TPSs to accommodate GFPP; (2) type-A sester-TPSs have more aromatic residues (five or six) in their catalytic pocket than classic TPSs (two or three), which also determines whether the type-A or type-B cyclization mechanism is active; and (3) the other residues responsible for product fidelity are determined by interconversion of AtTPS18 and its close homologs. Altogether, this study improves our understanding of the catalytic mechanism of plant sester-TPS, which ultimately enables the rational engineering of sesterterpenoids for future applications., Sesterterpenoids, a relatively new group of terpenoids, are structurally diverse and widely distributed in bacteria, fungi, and the plant kingdom. However, the enzymatic mechanism of sesterterpene synthase (sester-TPS), the first committed biosynthesis step, remains obscure. This study reveals the critical amino acids controlling the substrate and product specificity of plant sester-TPS by determining the first crystal structure of the sester-TPS–FSPP complex.

Graphical abstract, Highlights • Study reveals specific dynamics of oncogenic K-Ras mutants G12C/V, G13D and Q61H. • P-loop mutations have pan-mutant and mutant-specific effects on local dynamics. • All active K-Ras P-loop mutations cause α3 helix to move away from Loop 7. • Only G12 mutations cause SII to move away from the α3 helix and the P-loop. • All studied mutations cause the α2 of SII region to get closer to C-terminal of α3., K-Ras is the most frequently mutated protein in human cancers. However, until very recently, its oncogenic mutants were viewed as undruggable. To develop inhibitors that directly target oncogenic K-Ras mutants, we need to understand both their mutant-specific and pan-mutant dynamics and conformations. Recently, we have investigated how the most frequently observed K-Ras mutation in cancer patients, G12D, changes its local dynamics and conformations (Vatansever et al., 2019). Here, we extend our analysis to study and compare the local effects of other frequently observed oncogenic mutations, G12C, G12V, G13D and Q61H. For this purpose, we have performed Molecular Dynamics (MD) simulations of each mutant when active (GTP-bound) and inactive (GDP-bound), analyzed their trajectories, and compared how each mutant changes local residue conformations, inter-protein distance distributions, local flexibility and residue pair correlated motions. Our results reveal that in the four active oncogenic mutants we have studied, the α2 helix moves closer to the C-terminal of the α3 helix. However, P-loop mutations cause α3 helix to move away from Loop7, and only G12 mutations change the local conformational state populations of the protein. Furthermore, the motions of coupled residues are mutant-specific: G12 mutations lead to new negative correlations between residue motions, while Q61H destroys them. Overall, our findings on the local conformational states and protein dynamics of oncogenic K-Ras mutants can provide insights for both mutant-selective and pan-mutant targeted inhibition efforts.

Many repetitive elements of the human genome have been related to neurodegenerative diseases. Insights into evolution and function of genomes contribute to understanding of the genetics of human diseases in relation to medical outcome that is often not straightforward. Search for correlations takes into account the fact that repeated sequences adopt non-canonical DNA structures that are different from the double helix. G-rich DNA molecules can form inter- or intramolecular hydrogen bonds to form G-quartets. Vertical stacking of G-quartets results in a G-quadruplex structure. Remarkably, even when DNA sequence is the same, small differences such as concentration of DNA, concentration of cations and pH of solution may result in different structures. NMR spectroscopy has been a major method to uncover topologies of G-quadruplexes and discern equilibria among diverse folds. GGGGCC hexanucleotide repeats from C9orf72 gene adopt G-quadruplex structures that may serve as potential targets for structure-based design of a molecule directed toward amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). AGCGA-repeat sequences that are related to neurodevelopment and neurological disorders have been shown to form AGCGA-quadruplexes. Using NMR we have demonstrated that AGCGA-quadruplexes are stabilized by G-A and G-C base pairs forming GAGA- and GCGC-quartets connected with edge-type loops stabilized mostly by G-G base pairs in N1-carbonyl geometry. It is especially interesting that even though guanine residues are very common in oligonucleotides that form AGCGA-quadruplexes they in turn do not exhibit G-quartets and are insensitive to the presence of different cations such as K+, Na+ and NH4+. This property makes the AGCGA-quadruplex structural family unique compared to the related and more widely known family of G-quadruplexes.

Summary Ectodomain (EC) shedding defines the proteolytic removal of a membrane protein EC and acts as an important molecular switch in signaling and other cellular processes. Using tumor necrosis factor (TNF)α as a model substrate, we identify a non-canonical shedding activity of SPPL2a, an intramembrane cleaving aspartyl protease of the GxGD type. Proline insertions in the TNFα transmembrane (TM) helix strongly increased SPPL2a non-canonical shedding, while leucine mutations decreased this cleavage. Using biophysical and structural analysis, as well as molecular dynamic simulations, we identified a flexible region in the center of the TNFα wildtype TM domain, which plays an important role in the processing of TNFα by SPPL2a. This study combines molecular biology, biochemistry, and biophysics to provide insights into the dynamic architecture of a substrate's TM helix and its impact on non-canonical shedding. Thus, these data will provide the basis to identify further physiological substrates of non-canonical shedding in the future., Graphical Abstract, Highlights • SPPL2a acts a non-canonical sheddase on TNFα • Increased conformational flexibility of TNFα enhances non-canonical shedding • Decreased conformational flexibility of TNFα reduces non-canonical shedding, Biochemistry; Structural Biology; Biophysics

Graphical abstract, Protein-protein interactions (PPIs) play a key role in numerous biological processes. Many efforts have been undertaken to develop PPI modulators for therapeutic applications; however, to date, most of the peptide binders designed to target PPIs are derived from native binding helices or using the native helix binding site, which has limited the applications of protein-protein interface binding peptide design. Here, we developed a general computational algorithm, HPer (Helix Positioner), that locates single-helix binding sites at protein-protein interfaces based on the structure of protein targets. HPer performed well on known single-helix-mediated PPIs and recaptured the key interactions and hot-spot residues of native helical binders. We also screened non-helical-mediated PPIs in the PDBbind database and identified 17 PPIs that were suitable for helical peptide binding, and the helical binding sites in these PPIs were also predicted for designing novel peptide ligands. The L2 domain of EGFR, which was the top ranked, was selected as an example to show the protocol and results of designing novel helical peptide ligands on the searched binding site. The binding stability of the designed sequences were further investigated using molecular dynamics simulations.

SUMMARY Piezo proteins form mechanically activated ion channels that are responsible for our sense of light touch, proprioception, and vascular blood flow. Upon activation by mechanical stimuli, Piezo channels rapidly inactivate in a voltage-dependent manner through an unknown mechanism. Inactivation of Piezo channels is physiologically important, as it modulates overall mechanical sensitivity, gives rise to frequency filtering of repetitive mechanical stimuli, and is itself the target of numerous human disease-related channelopathies that are not well understood mechanistically. Here, we identify the globular C-terminal extracellular domain as a structure that is sufficient to confer the time course of inactivation and a single positively charged lysine residue at the adjacent inner pore helix as being required for its voltage dependence. Our results are consistent with a mechanism for inactivation that is mediated through voltage-dependent conformations of the inner pore helix and allosteric coupling with the C-terminal extracellular domain., In Brief Wu et al. examine how the properties of inactivation are influenced in mechanically activated Piezo ion channels. They identify two structural domains, the C-terminal extracellular domain and the inner pore helix, that correspond with the kinetics and voltage dependence of inactivation, respectively.

Serum- and glucocorticoid-inducible kinase 1 (SGK1), a protein kinase, shares significant structural similarity with other members of the AGC protein kinase family. It has been reported that the inactive SGK1 structure lacks αC helix and this unique feature makes it distinct from other protein kinases. Activation of SGK1 by PDK1 requires phosphorylation at Thr256, but the structural insights of the activation remain unclear. The co-crystal structures of small molecule inhibitors, Magnesium (Mg+2) and ATP bound to the inactive SGK1 are reported however the important regulatory domains such as αC helix are missing in these crystal structures. We modelled the missing αC domain and employed computational molecular dynamics simulations to study the conformational changes in the WT and phosphorylated human SGK1 to systematically investigate how the individual domain motions are modulated by the binding of substrate and Mg+2. The MD results corroborate with the experiential findings and has shown that the inactive SGK1 lacks αC helix content. Surprisingly, we find that the active SGK1 structure closely resembles with other protein kinases and adopt the αC helix content up on SGK1 phosphorylation. However, the residues participating in αC helix formation are fewer than reported in protein kinase A structure, a close relative of SGK1. The computational binding analysis reveals that most of the SGK1 selective inhibitors have less binding affinity for active SGK1 than some FDA-approved kinase inhibitors such as Afatinib, Tofacitinib, Dabrafenib, and Palbociclib. Only EMD638683 was seen as a strong candidate for selective SGK1 inhibition. To our knowledge, this is the first dynamic study of SGK1 that provides new structural insights around the active site that would surely help the experimental biologists for the design of suitable selective ligands able to inhibit or activate SGK1 function.

The antihypertensive potential of a land snail by-product hydrolysate (SBH), obtained after an industrial treatment of the raw material, was studied in vitro and in vivo . The ACE inhibitory activity of SBH was characterised by an IC 50 value of 23 µg⋅mL −1 , which was not affected by in vitro digestion. SBH enhanced the Caco-2 intestinal cell metabolic activity and did not induce any toxicity in Wistar rats. The partial purification of SBH led to the obtainment of an active fraction characterised by an IC 50 of 0.007 µg⋅mL −1 . The sequences of the 17 most abundant peptides of the fraction were identified by LC/MS/MS analysis. Seven of them (YG, YA, VY, SF, FG, GF and VW) are known ACE inhibitory peptides. Finally, in vivo study on SHR rats showed that SBH significantly reduced systolic blood pressure. SBH represents therefore a new candidate as an ingredient for the design of functional foods against hypertension.

Some fundamental molecules of life are suggested to have been formed, proliferated, and evolved through photochemical microscopic dissipative structuring and autocatalytic proliferation under the UV-C/UV-B solar environment prevalent at Earth’s surface throughout the Archean. Evidence is given in the numerous salient characteristics of these, including their strong absorption in this spectral region and their rapid non-radiative excited state decay through inherent conical intersections. The examples of the dissipative structuring and dissipative proliferation of the purines and of single strand DNA are given. UV-C and UV-B-induced stationary state isomerizations and tautomerizations are shown to be crucial to the formation of the purines from hydrogen cyanide in an aqueous environment under UV-C light, while UV-C induced phosphorylation of nucleosides and denaturing of double helix RNA and DNA are similarly important to the production and proliferation of single strand DNA. This thermodynamic dissipation perspective provides a physical-chemical foundation for understanding the origin and evolution of life.

Prion diseases, or transmissible spongiform encephalopathies, are a group of rare fatal neurodegenerative maladies that affect humans and animals. The main event in disease progression is the posttranslational conversion of the ubiquitously expressed cellular form of the prion protein (PrPC) into its misfolded and pathogenic isoform, known as prion or PrPSc. In the presence of specific disease-linked mutations, the conversion may occur spontaneously. Molecular simulation studies on human PrPC wild-type and variants from several research groups, including ours, have provided a consistent picture of the effect of such mutations. In particular, the calculations have pinpointed “hot spots” for the conversion across several disease-linked variants. They have also identified a region of the protein containing two helices (Helix 2 and Helix 3) as a key structural element most prone to the conversion, consistently with a wealth of experimental data. Some of these findings are summarized here.

Watson and Crick’s revolutionary discovery in 1953 of the double-stranded helical structure of DNA is described, including the crucial contributions of Pauling, Chargaff, and especially the X-ray photographs of Franklin. One of the exciting aspects of the Watson–Crick model of DNA is that it suggested an hypothesis for the replication of genetic material, so that it can accurately be passed down from generation to generation.

G protein-coupled receptors (GPCRs) are membrane proteins critical in cellular signaling, making them important targets for therapeutics. The activation of GPCRs is central to their function, requiring multiple conformations of the GPCRs in their activation landscape. To enable rational design of GPCR-targeting drugs, it is essential to obtain the ensemble of atomistic structures of GPCRs along their activation pathways. This is most challenging for structure determination experiments, making it valuable to develop reliable computational structure prediction methods. In particular, since the active-state conformations are higher in energy (less stable) than inactive-state conformations, they are difficult to stabilize. In addition, the computational methods are generally biased toward lowest energy structures by design and miss these high energy but functionally important conformations. To address this problem, we have developed a computationally efficient ActiveGEnSeMBLE method that systematically predicts multiple conformations that are likely in the GPCR activation landscape, including multiple active- and inactive-state conformations. ActiveGEnSeMBLE starts with a systematic coarse grid sampling of helix tilts/rotations (~ 13 trillion transmembrane domain conformations) and identifies multiple potential active-state energy wells, using the TM3–TM6 intracellular distance as a surrogate activation coordinate. These energy wells are then sampled locally using a finer grid in conformational space to find a locally minimized conformation in each energy well, which can be further relaxed using molecular dynamics (MD) simulations. This method, combining homology modeling, hierarchical complete conformational sampling, and nanosecond scale MD, provides one of the very few computational methods that predict multiple candidates for active-state conformations and is one of the most computationally affordable.

De novo design has proven a powerful methodology for understanding protein folding and function, and for mimicking or even bettering the properties of natural proteins. Extensive progress has been made in the design of helical bundles, simple structural motifs that can be nowadays designed with a high degree of precision. Among helical bundles, the four-helix bundle is widespread in nature, and is involved in numerous and fundamental processes. Representative examples are the carboxylate bridged diiron proteins, which perform a variety of different functions, ranging from reversible dioxygen binding to catalysis of dioxygen-dependent reactions, including epoxidation, desaturation, monohydroxylation, and radical formation. The “Due Ferri” (two-irons; DF) family of proteins is the result of a de novo design approach, aimed to reproduce in minimal four-helix bundle models the properties of the more complex natural diiron proteins, and to address how the amino acid sequence modulates their functions. The results so far obtained point out that asymmetric metal environments are essential to reprogram functions, and to achieve the specificity and selectivity of the natural enzymes. Here, we describe a design method that allows constructing asymmetric four-helix bundles through the covalent heterodimerization of two different α-helical harpins. In particular, starting from the homodimeric DF3 structure, we developed a protocol for covalently linking the two α 2 monomers by using the Cu(I) catalyzed azide–alkyne cycloaddition. The protocol was then generalized, in order to include the construction of several linkers, in different protein positions. Our method is fast, low cost, and in principle can be applied to any couple of peptides/proteins we desire to link.

Starch is a fundamental nutrient that provides between 20% and 40% of energy for most individuals. Starch is a complex polymer of glucose, but starch-containing foods can provide significant fiber, protein, and micronutrients although these are highly variable. This article will examine the differences between the various starch polymers, the difference between highly refined sources of starch and less refined sources, and the major sources of starch - rice, wheat, maize, potatoes, sorghum, yam, cassava, plantains, rye, oats, barley, and legumes - and the health effects of these different sources. Refereed/Peer-reviewed

Oblivious manipulation of the device by the patient is referred to as “Twiddler's” syndrome. It is characterized by the coiling of the pacemaker lead due to the rotation of the pacemaker generator on its long axis. However, the rotation of the pacemaker generator on its transverse axis with subsequent coiling of the pacemaker leads around the pulse generator is called as ‘’Reel syndrome’’. In this case, we present a 69-year-old patient with ‘selective’ Reel syndrome and postulate the possible explanation for damaged atrial lead.

Ag nanowires and nanoparticles have been formed on hybrid λ-DNA/conducting polymer templates. The strong, but non-covalent, interaction of the conducting polymer with the double helix allowed us to incorporate chemical functionalities (alkynyl) into the DNA/conducting polymer strands by synthesis of functional monomers. Oxidative polymerisation of alkynyl-thienylpyrrole in the presence of λ-DNA produced conductive nanowires bearing alkyne groups; we show, using a combination of AFM, cAFM and EFM phase measurements that the alkyne functionality strong influences the subsequent templating reaction of Tollens’ reagent to produce uniform conductive nanowires comprised of many connected Ag clusters. Keywords: Nanowire, Conductive polymer, DNA, Template, Silver, Nanoparticle

Brucella abortus is an important pathogenic bacterium that has to overcome oxygen deficiency in order to achieve a successful infection. Previously, we proved that a two-component system formed by the histidine kinase NtrY and the response regulator NtrX is essential to achieve an adaptive response to low oxygen tension conditions. Even though the relevance of this signaling pathway has already been demonstrated in other microorganisms, its molecular activation mechanism has not yet been described in detail. In this article, we report the first crystal structures from different conformations of the NtrX receiver domain from B. abortus, and we propose a sequence of events to explain the structural rearrangements along the activation process. The analysis of the structures obtained in the presence of the phosphoryl group analog beryllofluoride led us to postulate that changes in the interface formed by the α4 helix and the β5 strand are important for the activation, producing a reorientation of the α5 helix. Also, a biochemical characterization of the NtrX receiver domain enzymatic activities was performed, describing its autophosphorylation and autodephosphorylation kinetics. Finally, the role of H85, an important residue, was addressed by site-directed mutagenesis. Overall, these results provide significant structural basis for understanding the response regulator activation in this bacterial two-component system. Fil: Fernandez, Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Otero, Lisandro Horacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Plataforma Argentina de Biología Estructural y Metabolómica PLABEM; Argentina Fil: Klinke, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Plataforma Argentina de Biología Estructural y Metabolómica PLABEM; Argentina Fil: Carrica, Mariela del Carmen. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Goldbaum, Fernando Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Plataforma Argentina de Biología Estructural y Metabolómica PLABEM; Argentina

Riboswitches are RNA sequences located in noncoding portions of mRNA that can sense specific ligands and subsequently control gene expression. The ligand-binding event induces conformational changes in the riboswitch that are then transmitted to the gene expression apparatus. Probing the mechanisms of such a fine regulation at atomic resolution is very difficult experimentally and molecular dynamics (MD) could be used to quantify the ligand-dependent behavior of a riboswitch. However, since the accessible time scale of fully atomistic simulations is limited, this can only be done using enhanced sampling techniques. Here, we discuss the application of steered MD to the characterization of the ligand-dependent stability of the aptamer terminal helix in the add adenine-sensing riboswitch. The employed techniques are discussed in detail and sample input files are provided. We show that with a limited computational effort it is possible to quantify, in terms of free energy, the stacking interaction between the ligand and the terminal helix, obtaining results in agreement with thermodynamic experiments.

While EPR allows for the characterization of protein structure and function due to its exquisite sensitivity to spin label dynamics, orientation, and distance, these measurements are often limited in sensitivity due to the use of labels that are attached via flexible monofunctional bonds, incurring additional disorder and nanosecond dynamics. In this chapter, we present methods for using a bifunctional spin label (BSL) to measure muscle protein structure and dynamics. We demonstrate that bifunctional attachment eliminates nanosecond internal rotation of the spin label, thereby allowing the accurate measurement of protein backbone rotational dynamics, including microsecond-to-millisecond motions by saturation transfer EPR. BSL also allows for accurate determination of helix orientation and disorder in mechanically and magnetically aligned systems, due to the label's stereospecific attachment. Similarly, labeling with a pair of BSL greatly enhances the resolution and accuracy of distance measurements measured by double electron-electron resonance (DEER). Finally, when BSL is applied to a protein with high helical content in an assembly with high orientational order (e.g., muscle fiber or membrane), two-probe DEER experiments can be combined with single-probe EPR experiments on an oriented sample in a process we call BEER, which has the potential for ab initio high-resolution structure determination.

The cross section of a flexible pipe is a combined construction of armor layers, which usually are of spirally wound steel tendons, and sealing layers, which are polymers of thermoplastic materials or compliant steel tubes. The helix armor components are applied in layers with a given lay angle, which is different significantly in the different armor components. The number of layers and properties of each layer are selected to meet the design requirements. The complex design of unbonded flexible pipe leads to the difficulty in its analysis. In this chapter, the design guidelines are presented first. Then, the material and mechanical properties of flexible pipe components are introduced. And the local cross-section analysis and global dynamic analysis, capturing flexible pipe structural response under different loads, are summarized.

Ionic-complementary peptides (ICPs) are well-known for their extraordinary ability to self-assemble into amyloid-like fibrils due to their high propensity to form β-sheet structures. These self-assembled fibrils have many potential applications, such as templates for nanowire fabrication, platforms or scaffolds for tissue engineering, delivery of proteins and peptide medicines and biologic surface engineering. Combining experimental efforts and all-atom molecular dynamics simulations, we designed an ionic-complementary sequence (Ac-EMK8II-CONH2) to form unique α-helical structures instead of conventional β-sheets. Such a α-helical ICP is intriguing not only in its secondary structure but also in its unusual capability in assembling into novel twisted-ribbon-like nanofibrils which could have potential applications as new biomaterials. Our results also indicate that fine tuning in the sequences of an ICP is critical to the final assembled structures and should be carefully considered in the peptide design.

Compared with cylindrical worms, planar double enveloping hourglass worms (TP worms) have plenty of advantages. The measurement of TP worms is a key problem limiting the application of the worms. With regards to this, we present a measurement method for TP worms and develop a special worm measuring machine which can achieve the purpose of measuring geometric deviations. The working principle and constitution of the machine are introduced, and the principle of the measurement based on the mathematical model of each geometric deviation is explained in detail. An example of helix deviation measurement shows the whole process of the measurement.

The inverse relationship between high density lipoprotein (HDL) plasma levels and coronary heart disease has been attributed to the role that HDL and its major constituent, apolipoprotein A-I (apoA-I), play in reverse cholesterol transport (RCT). The efficiency of RCT depends on the specific ability of apoA-I to promote cellular cholesterol efflux, bind lipids, activate lecithin:cholesterol acyltransferase (LCAT), and form mature HDL that interact with specific receptors and lipid transfer proteins. From the intensive analysis of apoA-I secondary structure has emerged our current understanding of its different classes of amphipathic α-helices, which control lipid-binding specificity. The main challenge now is to define apoA-I tertiary structure in its lipid-free and lipid-bound forms. Two models are considered for discoidal lipoproteins formed by association of two apoA-I with phospholipids. In the first or picket fence model, each apoA-I wraps around the disc with antiparallel adjacent α-helices and with little intermolecular interactions. In the second or belt model, two antiparallel apoA-I are paired by their C-terminal α-helices, wrap around the lipoprotein, and are stabilized by multiple intermolecular interactions. While recent evidence supports the belt model, other models, including hybrid models, cannot be excluded. ApoA-I α-helices control lipid binding and association with varying levels of lipids. The N-terminal helix 44–65 and the C-terminal helix 210–241 are recognized as important for the initial association with lipids. In the central domain, helix 100–121 and, to a lesser extent, helix 122–143, are also very important for lipid binding and the formation of mature HDL, whereas helices between residues 144 and 186 contribute little. The LCAT activation domain has now been clearly assigned to helix 144–165 with secondary contribution by helix 166–186. The lower lipid binding affinity of the region 144–186 may be important to the activation mechanism allowing displacement of these apoA-I helices by LCAT and presentation of the lipid substrates. No specific sequence has been found that affects diffusional efflux to lipid-bound apoA-I. In contrast, the C-terminal helices, known to be important for lipid binding and maintenance of HDL in circulation, are also involved in the interaction of lipid-free apoA-I with macrophages and specific lipid efflux. While much progress has been made, other aspects of apoA-I structure–function relationships still need to be studied, particularly its lipoprotein topology and its interaction with other enzymes, lipid transfer proteins and receptors important for HDL metabolism.—Frank, P. G., and Y. L. Marcel. Apolipoprotein A-I: structure–function relationships. J. Lipid Res. 2000. 41: 853–872.

Apicomplexan parasites enter host cells by many sophisticated steps including use of an ATP-powered invasion machinery. The machinery consists of multiple proteins, including a special myosin (MyoA) which moves along an actin fiber and which is connected to the myosin tail interaction protein (MTIP). Here we report a crystal structure of the major MyoA-binding domain (D3) of Plasmodium falciparum MTIP in complex with an anti-MTIP nanobody. In this complex, the MyoA-binding groove in MTIP-D3 is considerably less accessible than when occupied by the MyoA helix, due to a shift of two helices. The nanobody binds to an area slightly overlapping with the MyoA binding groove, covering a hydrophobic region next to the groove entrance. This provides a new avenue for arriving at compounds interfering with the invasion machinery since small molecules binding simultaneously to the nanobody binding site and the adjacent MyoA binding groove would prevent MyoA binding by MTIP.

Protoglobin is the first globin identified in Archaea; its biological role is still unknown, although it can bind O2, CO and NO reversibly in vitro. The X-ray structure of Methanosarcina acetivorans protoglobin revealed several peculiar structural features. Its tertiary structure can be considered as an expanded version of the canonical globin fold, characterised by the presence of a pre-A helix (named Z) and a 20-residue N-terminal extension. Other unusual trends are a large distortion of the haem moiety, and its complete burial in the protein matrix due to the extended CE and FG loops and the 20-residue N-terminal loop. Access of diatomic ligands to the haem has been proposed to be granted by two tunnels, which are mainly defined by helices B/G (tunnel 1) and B/E (tunnel 2), and whose spatial orientation and topology give rise to an almost orthogonal two-tunnel system unprecedented in other globins. At a quaternary level, protoglobin forms a tight dimer, mostly based on the inter-molecular four-helix bundle built by the G- and H-helices, similar to that found in globin-coupled sensor proteins, which share with protoglobin a common phylogenetic origin. Such unique structural properties, together with an unusually low O2 dissociation rate and a selectivity ratio for O2/CO binding that favours O2 ligation, make protoglobin a peculiar case for gaining insight into structure to function relationships within the globin superfamily. While recent structural and biochemical data have given answers to important questions, the functional issue is still unclear and it is expected to represent the major focus of future investigations.

MYCOM and HOLROYD have studied noise and vibration reduction in medium-size oil-flooded twin-screw compressor in collaboration. The oil-flooded twin-screw compressor works with lobe contact between male and female rotors. Rotor misalignments in operation lead to transmission errors which can excite noise and vibration. In this study, rotor misalignments of a target machine were estimated and helix modifications which absorb the bad influence of these misalignments were designed by using transmission error simulation. As a result of experiment of prototype rotors, a reduction in the noise and vibration was confirmed under target conditions and part load conditions.

Recently developed X-ray crystal structures of active state G-protein-coupled receptors have opened the way for detailed examination of the movement of the transmembrane (TM) helices and the specific residues involved in the receptor activation upon ligand binding. Previous modeling studies have indicated that the brain cannabinoid (CB1) receptor binds with a ligand at least in part through a hydrophobic tail on the ligand. This interaction is believed to be similar to the rotameric toggle switch proposed for the β2 adrenergic receptor (β2AR). In the present study, an active state model for the CB1 receptor, guided by the X-ray structure of the active state for β2AR, was constructed with HU210 bound as a ligand. Molecular dynamics (MD) simulations were employed to provide a smooth progression between inactive and active states of the receptor. This model was compared with our previously published CB1 receptor model to identify the functional residues that play key roles in triggering receptor conformational changes upon agonist binding. Movements in TM helices and functional residues are discussed. W279 5.43 , contributing to an inward movement of the fifth TM helix (TM5) to the helical core, could serve as another rotameric switch for receptor activation. V282 5.46 , interacting with the ligand's hydrophobic C3 alkyl chain, appears to play a key role in TM5 inward movement centered at L286 5.50 and subsequent coupling to V204 3.40 . V204 3.40 , closely interacting with the TM5 and TM6 hydrophobic patch residues in the middle of the receptor, particularly I290 5.54 and L352 6.44 , appears to facilitate helical rearrangements, leading to the breakage of the ionic lock and the rotameric change of Y397 7.53 , which are key features of the active state.