Home About us Contact
|
Home About us Contact | ||
|
|
||
Internal Cavities (internal + cavity)
Selected AbstractsPolyoxometalates with Internal Cavities: Redox Activity, Basicity, and Cation Encapsulation in [Mn+P5W30O110](15-n)- Preyssler Complexes, with M: Na+, Ca2+, Y3+, La3+, Ce3+, and Th4+.CHEMINFORM, Issue 50 2007Jorge A. Fernandez Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF. [source] Encapsulation and Stabilization of Reactive Aromatic Diazonium Ions and the Tropylium Ion Within a Supramolecular HostEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 24 2004Julia L. Brumaghim Abstract Supramolecular assemblies with internal cavities are being developed as nanoscale reaction vessels to protect or modify the reactivity of guest species through encapsulation. Diazonium cations and the tropylium cation were examined for their ability to encapsulate in the tetrahedral [Ga4L6]12, supramolecular assembly. The 4-(diethylamino)benzenediazonium cation 1 readily formed a 1:1 host,guest complex with this assembly, and this encapsulation prevented 1 from reacting with 2,4-pentanedione in D2O. The tropylium cation also formed a 1:1 host,guest complex with the [Ga4L6]12, assembly, greatly slowing its decomposition in D2O. Encapsulation in the protected environment of this host cavity alters the reactivity of these guest molecules, giving them greater stability. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] A novel thermostable hemoglobin from the actinobacterium Thermobifida fuscaFEBS JOURNAL, Issue 16 2005Alessandra Bonamore The gene coding for a hemoglobin-like protein (Tf-trHb) has been identified in the thermophilic actinobacterium Thermobifida fusca and cloned in Escherichia coli for overexpression. The crystal structure of the ferric, acetate-bound derivative, was obtained at 2.48 Å resolution. The three-dimensional structure of Tf-trHb is similar to structures reported for the truncated hemoglobins from Mycobacterium tuberculosis and Bacillus subtilis in its central domain. The complete lack of diffraction patterns relative to the N- and C-terminal segments indicates that these are unstructured polypeptides chains, consistent with their facile cleavage in solution. The absence of internal cavities and the presence of two water molecules between the bound acetate ion and the protein surface suggest that the mode of ligand entry is similar to that of typical hemoglobins. The protein is characterized by higher thermostability than the similar mesophilic truncated hemoglobin from B. subtilis, as demonstrated by far-UV CD melting experiments on the cyano-met derivatives. The ligand-binding properties of Tf-trHb, analyzed in stopped flow experiments, demonstrate that Tf-trHb is capable of efficient O2 binding and release between 55 and 60 °C, the optimal growth temperature for Thermobifida fusca. [source] Enveloping triangulation method for detecting internal cavities in proteins and algorithm for computing their surface areas and volumesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2009Ján Bu Abstract Detection and quantitative characterization of the internal cavities in proteins remain an important topic in studying protein structure and function. Here we propose a new analytical method for detecting the existence of cavities in proteins. The method is based on constructing the special enveloping triangulation enclosing the cavities. Based on this method, we develop an algorithm and a fortran package, CAVE, for computing volumes and surface areas of cavities in proteins. We first test our method and algorithm in some artificial systems of spheres and find that the calculated results are consistent with exact results. Then we apply the package to compute volumes and surface areas of cavities for some protein structures in the Protein Data Bank. We compare our calculated results with those obtained by some other methods and find that our approach is reliable. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Mesophyll conductance to CO2: current knowledge and future prospectsPLANT CELL & ENVIRONMENT, Issue 5 2008JAUME FLEXAS ABSTRACT During photosynthesis, CO2 moves from the atmosphere (Ca) surrounding the leaf to the sub-stomatal internal cavities (Ci) through stomata, and from there to the site of carboxylation inside the chloroplast stroma (Cc) through the leaf mesophyll. The latter CO2 diffusion component is called mesophyll conductance (gm), and can be divided in at least three components, that is, conductance through intercellular air spaces (gias), through cell wall (gw) and through the liquid phase inside cells (gliq). A large body of evidence has accumulated in the past two decades indicating that gm is sufficiently small as to significantly decrease Cc relative to Ci, therefore limiting photosynthesis. Moreover, gm is not constant, and it changes among species and in response to environmental factors. In addition, there is now evidence that gliq and, in some cases, gw, are the main determinants of gm. Mesophyll conductance is very dynamic, changing in response to environmental variables as rapid or even faster than stomatal conductance (i.e. within seconds to minutes). A revision of current knowledge on gm is presented. Firstly, a historical perspective is given, highlighting the founding works and methods, followed by a re-examination of the range of variation of gm among plant species and functional groups, and a revision of the responses of gm to different external (biotic and abiotic) and internal (developmental, structural and metabolic) factors. The possible physiological bases for gm, including aquaporins and carbonic anhydrases, are discussed. Possible ecological implications for variable gm are indicated, and the errors induced by neglecting gm when interpreting photosynthesis and carbon isotope discrimination models are highlighted. Finally, a series of research priorities for the near future are proposed. [source] CO migration pathways in cytochrome P450cam studied by molecular dynamics simulationsPROTEIN SCIENCE, Issue 5 2007Liliane Mouawad Abstract Previous laser flash photolysis investigations between 100 and 300 K have shown that the kinetics of CO rebinding with cytochrome P450cam(camphor) consist of up to four different processes revealing a complex internal dynamics after ligand dissociation. In the present work, molecular dynamics simulations were undertaken on the ternary complex P450cam(cam)(CO) to explore the CO migration pathways, monitor the internal cavities of the protein, and localize the CO docking sites. One trajectory of 1 nsec with the protein in a water box and 36 trajectories of 1 nsec in the vacuum were calculated. In each trajectory, the protein contained only one CO ligand on which no constraints were applied. The simulations were performed at 200, 300, and 320 K. The results indicate the presence of seven CO docking sites, mainly hydrophobic, located in the same moiety of the protein. Two of them coincide with xenon binding sites identified by crystallography. The protein matrix exhibits eight persistent internal cavities, four of which corresponding to the ligand docking sites. In addition, it was observed that water molecules entering the protein were mainly attracted into the polar pockets, far away from the CO docking sites. Finally, the identified CO migration pathways provide a consistent interpretation of the experimental rebinding kinetics. [source] Binding of the volatile general anesthetics halothane and isoflurane to a mammalian ,-barrel proteinFEBS JOURNAL, Issue 2 2005Jonas S. Johansson A molecular understanding of volatile anesthetic mechanisms of action will require structural descriptions of anesthetic,protein complexes. Porcine odorant binding protein is a 157 residue member of the lipocalin family that features a large ,-barrel internal cavity (515 ± 30 Å3) lined predominantly by aromatic and aliphatic residues. Halothane binding to the ,-barrel cavity was determined using fluorescence quenching of Trp16, and a competitive binding assay with 1-aminoanthracene. In addition, the binding of halothane and isoflurane were characterized thermodynamically using isothermal titration calorimetry. Hydrogen exchange was used to evaluate the effects of bound halothane and isoflurane on global protein dynamics. Halothane bound to the cavity in the ,-barrel of porcine odorant binding protein with dissociation constants of 0.46 ± 0.10 mm and 0.43 ± 0.12 mm determined using fluorescence quenching and competitive binding with 1-aminoanthracene, respectively. Isothermal titration calorimetry revealed that halothane and isoflurane bound with Kd values of 80 ± 10 µm and 100 ± 10 µm, respectively. Halothane and isoflurane binding resulted in an overall stabilization of the folded conformation of the protein by ,0.9 ± 0.1 kcal·mol,1. In addition to indicating specific binding to the native protein conformation, such stabilization may represent a fundamental mechanism whereby anesthetics reversibly alter protein function. Because porcine odorant binding protein has been successfully analyzed by X-ray diffraction to 2.25 Å resolution [1], this represents an attractive system for atomic-level structural studies in the presence of bound anesthetic. Such studies will provide much needed insight into how volatile anesthetics interact with biological macromolecules. [source] Opal Gels Templated Synthesis of Structured Titania Materials,MACROMOLECULAR RAPID COMMUNICATIONS, Issue 20 2004Jianhua Rong Abstract Summary: Core/shell opal gels of sulfonated polystyrene were used as templates to synthesize structured crystalline titania materials. Under acidic conditions, opal materials with hollow spheres of controllable shell thickness and cavity size were prepared. Under neutral conditions, inverse opal inorganic materials with a tunable pore size were prepared. It is crucial that proton ions induce a preferential sol/gel process, forming titania in the gel. Scanning electron micrograph of the interior region of a structured titania material derived from the G1 template used here. The inset shows broken spheres in which the internal cavity can be observed. [source] | ||||||||||