The structure of triple-stranded G-2C polynucleotide helices.

The thermal stability of a new polynucleotide complex has been used to establish the hydrogen-bonding structure of three-stranded C-G·CH⁺ helices. In the Hoogsteen structure, the 8NH₂ group of 8NH₂GMP can form a third hydrogen bond to the CH⁺ strand, but in the alternative structure, the 8NH₂ group can form no interbase hydrogen bonds. For the new complex, 8NH₂GMP·2 poly(C), a transition temperature of 80°C is observed under conditions in which the corresponding complex formed with 5′-GMP has a T_m of 20°C. We conclude from this 60° elevation of transition temperature that a third hydrogen bond is formed by the 8NH₂ group and that the structure must have Hoogsteen bonding. In order to be compatible with this structure in regular helices formed by U,C copolymers, A·2U bonding would also have to have a Hoogsteen structure.     

城市三维空间结构对碳排放影响的尺度效应

城市是碳排放最集中的区域,全面厘清城市空间结构对碳排放的影响对碳减排规划具有重要意义。以往研究主要关注城市二维结构与碳排放的关系,表明城市扩张是碳排放剧增的主要原因。虽然城市三维空间结构也会显著影响碳排放,然而其影响的尺度效应依然缺少深入分析。为此以广州市为例,结合相关性分析、随机森林探究三维空间结构与碳排放的关系,并揭示三维空间结构影响的尺度效应。研究结果表明：（1）（高层）建筑物密度、建筑覆盖率、容积率与人口密度是碳排放的关键影响因素,主要通过直接增加人类活动或加剧热岛效应使得能源消耗和碳排放增多;（2）三维空间结构对碳排放的影响具有明显的尺度效应。随着分析尺度的变化,碳排放受三维空间结构的不同方面主导;（3）广州作为紧凑型城市的代表,如果片面追求城市三维空间的紧凑布局将不利于低碳城市的发展。因此,相关部门应重视宏观尺度下的三维空间结构的合理布局,合理开发城市边缘地区,降低城市中心建筑物的紧凑布局,构建多中心的城市格局,以有效降低碳排放水平,促进低碳城市的构建与可持续发展。研究所得成果可为城市建筑三维空间布局的合理优化提供参考依据,助力"双碳"目标的实现。     

Structural insights into PDZ-mediated interaction of NHERF2 and LPA2, a cellular event implicated in CFTR channel regulation

The formation of CFTR–NHERF2–LPA₂ macromolecular complex in airway epithelia regulates CFTR channel function and plays an important role in compartmentalized cAMP signaling. We previously have shown that disruption of the PDZ-mediated NHERF2–LPA₂ interaction abolishes the LPA inhibitory effect and augments CFTR Cl⁻ channel activity in vitro and in vivo. Here we report the first crystal structure of the NHERF2 PDZ1 domain in complex with the C-terminal LPA₂ sequence. The structure reveals that the PDZ1–LPA₂ binding specificity is achieved by numerous hydrogen bonds and hydrophobic contacts with the last four LPA₂ residues contributing to specific interactions. Comparison of the PDZ1–LPA₂ structure to the structure of PDZ1 in complex with a different peptide provides insights into the diverse nature of PDZ1 substrate recognition and suggests that the conformational flexibility in the ligand binding pocket is involved in determining the broad substrate specificity of PDZ1. In addition, the structure reveals a small surface pocket adjacent to the ligand-binding site, which may have therapeutic implications. This study provides an understanding of the structural basis for the PDZ-mediated NHERF2–LPA₂ interaction that could prove valuable in selective drug design against CFTR-related human diseases.     

A unique structural feature of a phospholipase A2 is probed by molecular dynamics

The unusual catalytic network, revealed by the crystal structure of one of the two phospholipases A₂ (PLA₂) from the venom of the crotalid A.p.piscivorus has been probed using molecular dynamics. The catalytic network has been remodeled to a conformation similar to that found in all other PLA₂, and the modeled structure has been submitted to energy minimization and molecular dynamics simulation, to explore the conformational space of the network. The calculations have yielded a large reorganization of the catalytic network, which gets a conformation close to that of the crystal structure. These results suggest that the unusual catalytic network observed in the studied PLA₂ is a structural feature of the protein and not a crystal artifact.     

Solution Structure of the HIV Protease Inhibitor Acetyl-pepstatin as Determined by NMR and Molecular Modeling

Abstract

The structure of acetyl-pepstatin has been investigated in solution by two-dimensional NMR spectroscopy and molecular modeling. The analysis of DQFCOSY, TOCSY and NOESY spectra lead to a full assignment of the NMR signals both in DMSO-d₆ and in TFE-d₃:H₂O 1:1. Interproton distances, dihedral angles and exchange regimes of NH or OH protons were derived from ROESY connectivities, coupling constants and temperature dependences of the chemical shifts, respectively. Molecular modeling using the NMR distance and dihedral angle constraints obtained in DMSO-d₆ yielded a model showing a well-defined structure for the N-terminal segment Ac-1 to Sta-4, but a flexible structure for the C-terminal segment. The structure was less defined in TFE-d₃:H₂O 1:1 and ¹³C T₁ measurements are indicative of higher mobility. Comparison of the NMR-determined solution structure of acetyl-pepstatin with its crystal structure when bound to HIV-1 protease shows that the conformation is more extended in the complex as a result of intermolecular interactions.     

First-principles investigation of the novel structure,elastic and thermodynamic properties of IrAl3 coating

IrAl₃ coating is a promising advanced functional material. However, the crystal structure and relevant properties of IrAl₃ remain controversy. Here, we apply the first-principles calculations to investigate the crystal structure, elastic and thermodynamic properties of IrAl₃. The phonon dispersion curves and phonon density of states of IrAl₃ are calculated. We find that the reported hexagonal structure (P63/mmc) is dynamically instable. However, three new phases: tetragonal (P4/mbm) and cubic (Pm-3n and Pm-3?m) structures are predicted. In particular, IrTi₃-type structure is a derivative cubic structure because Al atom occurs migration from (0, 0.50, 0.50) site to (0, 0.25, 0.50) site. IrTi₃-type derivative cubic structure shows high shear deformation resistance and high elastic stiffness in comparison to other three structures. The strong shear deformation resistance and high elastic stiffness are attributed to the symmetrical Ir–Al bond. However, AuCu₃-type structure shows the high Debye temperature and low heat capacity in comparison to other structures.     

The Solution Structure of the C-Terminal Ig-like Domain of the Bacteriophage λ Tail Tube Protein

Immunoglobulin (Ig)-like domains are found frequently on the surface of tailed double-stranded DNA bacteriophages, yet their functional role remains obscure. Here, we have investigated the structure and function of the C-terminal Ig-like domain of gpV (gpV_C), the tail tube protein of phage λ. This domain has been predicted through sequence similarity to be a member of the bacterial Ig-like domain 2 (Big_2) family, which is composed of more than 1300 phage and bacterial sequences. Using trypsin proteolysis, we have delineated the boundaries of gpV_C and have shown that its removal reduces the biological activity of gpV by 100-fold; thus providing a definitive demonstration of a functional role for this domain. Determination of the solution structure of gpV_C by NMR spectroscopy showed that it adopts a canonical Ig-like fold of the I-set class. This represents the first structure of a phage-encoded Ig-like domain and only the second structure of a Big_2 domain. Structural and sequence comparisons indicate that the gpV_C structure is more representative of both the phage-encoded Big_2 domains and Big_2 domains in general than the other available Big_2 structure. Bioinformatics analyses have identified two conserved clusters of residues on the surface of gpV_C that may be important in mediating the function of this domain.     

Alanine and proline content modulate global sensitivity to discrete perturbations in disordered proteins

Molecular transduction of biological signals is understood primarily in terms of the cooperative structural transitions of protein macromolecules, providing a mechanism through which discrete local structure perturbations affect global macromolecular properties. The recognition that proteins lacking tertiary stability, commonly referred to as intrinsically disordered proteins (IDPs), mediate key signaling pathways suggests that protein structures without cooperative intramolecular interactions may also have the ability to couple local and global structure changes. Presented here are results from experiments that measured and tested the ability of disordered proteins to couple local changes in structure to global changes in structure. Using the intrinsically disordered N‐terminal region of the p53 protein as an experimental model, a set of proline (PRO) and alanine (ALA) to glycine (GLY) substitution variants were designed to modulate backbone conformational propensities without introducing non‐native intramolecular interactions. The hydrodynamic radius (R_h) was used to monitor changes in global structure. Circular dichroism spectroscopy showed that the GLY substitutions decreased polyproline II (PP_II) propensities relative to the wild type, as expected, and fluorescence methods indicated that substitution‐induced changes in R_h were not associated with folding. The experiments showed that changes in local PP_II structure cause changes in R_h that are variable and that depend on the intrinsic chain propensities of PRO and ALA residues, demonstrating a mechanism for coupling local and global structure changes. Molecular simulations that model our results were used to extend the analysis to other proteins and illustrate the generality of the observed PRO and alanine effects on the structures of IDPs. Proteins 2014; 82:3373–3384. © 2014 Wiley Periodicals, Inc.     

Structure and mode of action of a mosquitocidal holotoxin

The crystal structure of the full mosquitocidal toxin from Bacillus sphaericus (MTX_holo) has been determined at 2.5 Å resolution by the molecular replacement method. The resulting structure revealed essentially the complete chain consisting of four ricin B-type domains curling around the catalytic domain in a hedgehog-like assembly. As the structure was virtually identical in three different crystal packings, it is probably not affected by packing contacts. The structure of MTX_holo explains earlier autoinhibition data. An analysis of published complexes comprising ricin B-type lectin domains and sugar molecules shows that the general construction principle applies to all four lectin domains of MTX_holo, indicating 12 putative sugar-binding sites. These sites are sequence-related to those of the cytotoxin pierisin from cabbage butterfly, which are known to bind glycolipids. It seems therefore likely that MTX_holo also binds glycolipids. The seven contact interfaces between the five domains are predominantly polar and not stronger than common crystal contacts so that in an appropriate environment, the multidomain structure would likely uncurl into a string of single domains. The structure of the isolated catalytic domain plus an extended linker was established earlier in three crystal packings, two of which showed a peculiar association around a 7-fold axis. The catalytic domain of the reported MTX_holo closely resembles all three published structures, except one with an appreciable deviation of the 40 N-terminal residues. A comparison of all structures suggests a possible scenario for the translocation of the toxin into the cytosol.     

The complexation between holothurian triterpene glycosides and Chl as the basis for lipid-saponin carriers of subunit protein antigens

The ability of holothurian triterpene glycosides (cucumarioside A₂-2 from Cucumaria japonica, cucumarioside G₁ from C. fraudatrix, frondoside A from C. frondosa, and holotoxin A₁ from Apostichopus japonicus) to form supramolecular lipid-saponin complexes was studied. TEM demonstrated that all the studied compounds form supramolecular cholesterol-saponin complexes (nanoparticles) in aqueous medium. The complexes formed by cucumarioside A₂-2, holotoxin A₁, and frondoside A had a tubular structure and fundamentally differed in the structure from the particles produced by cucumarioside G₁. The morphology of the nanoparticles formed by cucumarioside A₂-2, holotoxin A₁, and cucumarioside G₁ changed depending on the fraction of cholesterol in the lipid-saponin system; however, this pattern was not observed for frondoside A. At the same molar fraction of cholesterol in the lipid-saponin system, cucumarioside A₂-2 formed the particles with the most pronounced tubular structure; the cholesterol-saponin complexes of holotoxin A₁ had a less pronounced tubular structure, whereas the structure of frondoside A particles was extremely heterogeneous. Comparative analysis of the morphology of the described supramolecular complexes and specific structural features of the glycosides demonstrated that the structure of the corresponding nanoparticles depended on the degree of branching of the carbohydrate moiety in the glycoside molecule and the complexation with cholesterol was determined by the specific features of aglycone structure. Thus, the feasibility of producing new generation antigen carriers using the complexes in question was proved.     

β-sheet to α-helix conversion and thermal stability of β-Galactosidase encapsulated in a nanoporous silica gel

The effect on protein conformation and thermal stability was studied for β-Galactosidase (β-Gal) encapsulated in the nanopores of a silicate matrix (E_β-Gal). Circular dichroism spectra showed that, compared with the enzyme in buffer (S_β-Gal), E_β-Gal exhibited a higher content of α-helix structure. Heating E_β-Gal up to 75?°C caused a decrease in the content of β-sheet structure and additional augments on E_β-Gal components attributed to helical content, instead of the generalized loss of the ellipticity signal observed with S_β-Gal. Steady state fluorescence spectroscopy analysis evidenced an E_β-Gal structure less compact and more accessible to solvent and also less stable against temperature increase. While for S_β-Gal the denaturation midpoint (Tm) was 59?°C, for E_β-Galit was 48?°C. The enzymatic activity assays at increasing temperatures showed that in both conditions, the enzyme lost most of its hydrolytic activity against ONPG at temperatures above 65?°C and E_β-Gal did it even at lower T values. Concluding, confinement in silica nanopores induced conformational changes on the tertiary/cuaternary structure of E_β-Gal leading to the loss of thermal stability and enzymatic activity.     

On the Structure of the Proton-Binding Site in the Fo Rotor of Chloroplast ATP Synthases

The recently reported crystal structures of the membrane-embedded proton-dependent c-ring rotors of a cyanobacterial F₁F_o ATP synthase and a chloroplast F₁F_o ATP synthase have provided new insights into the mechanism of this essential enzyme. While the overall features of these c-rings are similar, a discrepancy in the structure and hydrogen-bonding interaction network of the H⁺ sites suggests two distinct binding modes, potentially reflecting a mechanistic differentiation. Importantly, the conformation of the key glutamate side chain to which the proton binds is also altered. To investigate the nature of these differences, we use molecular dynamics simulations of both c-rings embedded in a phospholipid membrane. We observe that the structure of the c₁₅ ring from Spirulina platensis is unequivocally stable within the simulation time. By contrast, the proposed structure of the H⁺ site in the chloroplast c₁₄ ring changes rapidly and consistently into that reported for the c₁₅ ring, indicating that the latter represents a common binding mode. To assess this hypothesis, we have remodeled the c₁₄ ring by molecular replacement using the published structure factors. The resulting structure provides clear evidence in support of a common binding site conformation and is also considerably improved statistically. These findings, taken together with a sequence analysis of c-subunits in the ATP synthase family, indicate that the so-called proton-locked conformation observed in the c₁₅ ring may be a common characteristic not only of light-driven systems such as chloroplasts and cyanobacteria but also of a selection of other bacterial species.     

Solution NMR structure of Apo-calmodulin in complex with the IQ motif of human cardiac sodium channel NaV1.5

The function of the human voltage-gated sodium channel Na_V1.5 is regulated in part by intracellular calcium signals. The ubiquitous calcium sensor protein calmodulin (CaM) is an important part of the complex calcium-sensing apparatus in Na_V1.5. CaM interacts with an IQ (isoleucine-glutamine) motif in the large intracellular C-terminal domain of the channel. Using co-expression and co-purification, we have been able to isolate a CaM-IQ motif complex and to determine its high-resolution structure in absence of calcium using multi-dimensional solution NMR. Under these conditions, the Na_V1.5 IQ motif interacts with the C-terminal domain (C-lobe) of CaM, with the N-terminal domain remaining free in solution. The structure reveals that the C-lobe adopts a semi-open conformation with the IQ motif bound in a narrow hydrophobic groove. Sequence similarities between voltage-gated sodium channels and voltage-gated calcium channels suggest that the structure of the CaM-Na_V1.5 IQ motif complex can serve as a general model for the interaction between CaM and ion channel IQ motifs under low-calcium conditions. The structure also provides insight into the biochemical basis for disease-associated mutations that map to the IQ motif in Na_V1.5.     

Linking demographic responses and life history tactics from longitudinal data in mammals

In stochastic environments, a change in a demographic parameter can influence the population growth rate directly or via a resulting impact on age structure. Stochastic elasticity of the long‐run stochastic growth rate λ_s to a demographic parameter offers a suitable way to measure the overall demographic response because it includes both the direct effect of changing the demographic parameter and its indirect effect through changes in the age structure. From 25 mammalian populations with contrasting life histories, we investigated how pace of life and population growth rate influence the demographic responses (measured as the relative contributions of the direct and indirect components of stochastic elasticity on λ_s). We found that in short‐lived species, the change in population structure resulting from an increase in yearling survival leads to an additional increase in λ_s, whereas in long‐lived species, the same change in population structure leads to a decrease. Short‐lived species thus display a boom‐bust life history strategy contrary to long‐lived species, for which the long lifespan dampens the demographic consequences of changing age structure. Irrespective of the species’ life history strategy, the change in population age structure resulting from an increase in adult survival leads to an additional increase in λ_s due to an increase of the proportion of mature individuals in the population. On the contrary, a change in population age structure resulting from an increase of reproductive performance leads to a decrease in λ_s that is due to the increase of the proportion of immature individuals in the population. Our comparative analysis of stochastic elasticity patterns in mammals shows the existence of different demographic responses to changes in age structure between short‐ and long‐lived species, which improves our understanding of population dynamics in variable environments in relation to the species‐specific pace of life.     

C-terminal fragments of thymopoietin favor formation of F-actin bundles: Electron microscopic data

Electron microscopy showed that PEP₃₃, a synthetic peptide corresponding to the C-terminal part of the thymic hormone thymopoietin, favors bundling of F-actin filaments in the presence of 0.1 M KCl. The structure of PEP₃₃ aggregates located within bundles between actin filaments is very similar to the structure of aggregates visible in preparations of pure PEP₃₃. No changes were observed in the structure of G-actin in the presence of PEP₃₃. A similar though weaker bundling effect was also detected for PEP₅, or thymopentin, a fragment of PEP₃₃. This peptide favors the formation of bundles of actin filaments of small size. The possible role of aggregation of actin filaments under the action of thymopoietin peptides is discussed in the light of the fact that the systematic release of thymopoietin from thymus leads to a phenomenon characteristic of the serious neuromuscular disease myasthenia gravis.     

Prediction of Beta-Turn in Protein Using E-SSpred and Support Vector Machine

β-Turn is a secondary protein structure type that plays an important role in protein configuration and function. Here, we introduced an approach of β-turn prediction that used the support vector machine (SVM) algorithm combined with predicted secondary structure information. The secondary structure information was obtained by using E-SSpred, a new secondary protein structure prediction method. A 7-fold cross validation based on the benchmark dataset of 426 non-homologous protein chains was used to evaluate the performance of our method. The prediction results broke the 80% Q _total barrier and achieved Q _total = 80.9%, MCC = 0.44, and Q _predicted higher 0.9% when compared with the best method. The results in our research are coincident with the conclusion that β-turn prediction accuracy can be improved by inclusion of secondary structure information.     

Influence of carbon dioxide supply on the chloroplast structure of Chlorella pyrenoidosa

Summary Electron microscopic investigations show that the structure of the lamellar system of Chlorella pyrenoidosa depends on the carbon dioxide supply in the culture medium. Chloroplasts of C. pyrenoidosa when grown with 0.03% CO₂, show typical grana structure whereas with 3% CO₂ the chloroplast structure is typical of that of the Chlorophyceae.     

Some ambiguities in using the esr spectra of high-spin CoII species as “Structure Markers”

Co(ethylenethiourea)₂(CH₃CO₂)₂, with a pseudo-tetrahedral structure but having a long-bonded fifth ligand, gives an esr spectrum almost identical with that of Co-Bovine Carbonic Anhydrase-OH; a previous assignment of a similar structure to the Co^II-containing enzyme is then substantiated. Several other tetrahedral and trigonal-bipyramidal Co^II complexes have also been investigated. Although none gives δ values close to those of CoBCAOH and the correlation high δ = trigonal bipyramidal, low δ = tetrahedral seems to hold, the influence of even minor distortions within pseudo-tetrahedral symmetry on the esr spectra indicates that, used alone, esr spectra may not be an unambiguous structure marker for Co^II enzymes.