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1.
Complex I of respiratory chains plays a central role in bioenergetics and is implicated in many human neurodegenerative diseases. An understanding of its mechanism requires a knowledge of the organization of redox centers. The arrangement of iron-sulfur clusters in the hydrophilic domain of complex I from Thermus thermophilus has been determined with the use of x-ray crystallography. One binuclear and six tetranuclear clusters are arranged, maximally 14 angstroms apart, in an 84-angstrom-long electron transfer chain. The binuclear cluster N1a and the tetranuclear cluster N7 are not in this pathway. Cluster N1a may play a role in the prevention of oxidative damage. The structure provides a framework for the interpretation of the large amounts of data accumulated on complex I. 相似文献
2.
Abramson J Smirnova I Kasho V Verner G Kaback HR Iwata S 《Science (New York, N.Y.)》2003,301(5633):610-615
Membrane transport proteins that transduce free energy stored in electrochemical ion gradients into a concentration gradient are a major class of membrane proteins. We report the crystal structure at 3.5 angstroms of the Escherichia coli lactose permease, an intensively studied member of the major facilitator superfamily of transporters. The molecule is composed of N- and C-terminal domains, each with six transmembrane helices, symmetrically positioned within the permease. A large internal hydrophilic cavity open to the cytoplasmic side represents the inward-facing conformation of the transporter. The structure with a bound lactose homolog, beta-D-galactopyranosyl-1-thio-beta-D-galactopyranoside, reveals the sugar-binding site in the cavity, and residues that play major roles in substrate recognition and proton translocation are identified. We propose a possible mechanism for lactose/proton symport (co-transport) consistent with both the structure and a large body of experimental data. 相似文献
3.
Sikes HD Smalley JF Dudek SP Cook AR Newton MD Chidsey CE Feldberg SW 《Science (New York, N.Y.)》2001,291(5508):1519-1523
We measured rate constants of thermal, interfacial electron transfer through oligophenylenevinylene bridges between a gold electrode and a tethered redox species in contact with an aqueous electrolyte using the indirect laser-induced temperature jump technique. Analysis of the distance dependence indicates that, unlike other bridges studied to date, the rate constants are not limited by electronic coupling for bridges up to 28 angstroms long. The energy levels of the bridges relative to those of the redox species rule out hopping through the bridge. We conclude that, out to 28 angstroms, the transfer is limited by structural reorganization and that electron tunneling occurs in less than 20 picoseconds, suggesting that oligophenylenevinylene bridges could be useful for wiring molecular electronic elements. 相似文献
4.
Crystallographic structure of the octameric histone core of the nucleosome at a resolution of 3.3 A 总被引：13，自引：0，他引：13
R W Burlingame W E Love B C Wang R Hamlin H X Nguyen E N Moudrianakis 《Science (New York, N.Y.)》1985,228(4699):546-553
The structure of the (H2A-H2B-H3-H4)2 histone octamer has been determined by means of x-ray crystallographic techniques at a resolution of 3.3 angstroms. The octamer is a prolate ellipsoid 110 angstroms long and 65 to 70 angstroms in diameter, and its general shape is that of a rugby ball. The size and shape are radically different from those determined in earlier studies. The most striking feature of the histone octamer is its tripartite organization, that is, a central (H3-H4)2 tetramer flanked by two H2A-H2B dimers. The DNA helix, placed around the octamer in a path suggested by the features on the surface of the protein, appears like a spring holding the H2A-H2B dimers at either end of the (H3-H4)2 tetramer. 相似文献
5.
Crystals of CdGeO(3) grown at a pressure of 65 kilobars are tetragonal and have an ordered, garnet-like crystal structure with cadmium occupying the dodecahedral and octahedral sites, and germanium the octahedral and tetrahedral sites. The crystal structure (a = 12.406 +/- 1 angstroms, c = 12.256 +/- 1 angstroms, and space group 14,/a) has been refined by least-squares analysis to an R (discrepancy index) of 0.073. Two high-pressure phases of CaGeO(3) were synthesized, one isotypic with tetragonal CdGeO(3) (a = 12.514 +/- 3 angstroms, c = 12.358 +/- 3 angstroms), and the other isotypic with perovskite. 相似文献
6.
In situ synchrotron x-ray diffraction measurements of FeO at high pressures and high temperatures revealed that the high-pressure phase of FeO has the NiAs structure (B8). The lattice parameters of this NiAs phase at 96 gigapascals and 800 kelvin are a = 2.574(2) angstroms and c = 5.172(4) angstroms (the number in parentheses is the error in the last digit). Metallic behavior of the high-pressure phase is consistent with a covalently and metallically bonded NiAs structure of FeO. Transition to the NiAs structure of FeO would enhance oxygen solubility in molten iron. This transition thus provides a physiochemical basis for the incorporation of oxygen into the Earth's core. 相似文献
7.
Control of the selectivity of the aquaporin water channel family by global orientational tuning 总被引：1，自引：0，他引：1
Tajkhorshid E Nollert P Jensen MØ Miercke LJ O'Connell J Stroud RM Schulten K 《Science (New York, N.Y.)》2002,296(5567):525-530
Aquaporins are transmembrane channels found in cell membranes of all life forms. We examine their apparently paradoxical property, facilitation of efficient permeation of water while excluding protons, which is of critical importance to preserving the electrochemical potential across the cell membrane. We have determined the structure of the Escherichia coli aquaglyceroporin GlpF with bound water, in native (2.7 angstroms) and in W48F/F200T mutant (2.1 angstroms) forms, and carried out 12-nanosecond molecular dynamics simulations that define the spatial and temporal probability distribution and orientation of a single file of seven to nine water molecules inside the channel. Two conserved asparagines force a central water molecule to serve strictly as a hydrogen bond donor to its neighboring water molecules. Assisted by the electrostatic potential generated by two half-membrane spanning loops, this dictates opposite orientations of water molecules in the two halves of the channel, and thus prevents the formation of a "proton wire," while permitting rapid water diffusion. Both simulations and observations revealed a more regular distribution of channel water and an increased water permeability for the W48F/F200T mutant. 相似文献
8.
The existence of a monoclinic phase of hydroxyapatite, Ca(2)(PO(4))(4)OH, has been confirmed, by single-crystal structure analysis (weighted "reliability" factor = 3.9 percent on |F|(2)). The structure has space group P21/b, a = 9.4214(8) angstroms, b = 2a, c = 6.8814(7) angstroms, and gamma = 120 degrees , and is analogous to that of chlorapatite. The distortions from the hexagonal structure with which the monoclinic structure is pseudosymmetric are similar to those in chlorapatite, including enlargement of that triangular array of oxygen atoms in which the chlorine ion or, in hydroxyapatite, the hydroxyl hydrogen ion is approximately centered. The hydroxyapatite specimen was prepared by the conversion of a single crystal of chlorapatite in steam at 1200 degrees C, was mimetically twinned, and was approximately 37 percent monoclinic. 相似文献
9.
Halorhodopsin, an archaeal rhodopsin ubiquitous in Haloarchaea, uses light energy to pump chloride through biological membranes. Halorhodopsin crystals were grown in a cubic lipidic phase, which allowed the x-ray structure determination of this anion pump at 1.8 angstrom resolution. Halorhodopsin assembles to trimers around a central patch consisting of palmitic acid. Next to the protonated Schiff base between Lys(242) and the isomerizable retinal chromophore, a single chloride ion occupies the transport site. Energetic calculations on chloride binding reveal a combination of ion-ion and ion-dipole interactions for stabilizing the anion 18 angstroms below the membrane surface. Ion dragging across the protonated Schiff base explains why chloride and proton translocation modes are mechanistically equivalent in archaeal rhodopsins. 相似文献
10.
11.
Heine A DeSantis G Luz JG Mitchell M Wong CH Wilson IA 《Science (New York, N.Y.)》2001,294(5541):369-374
In classical enzymology, intermediates and transition states in a catalytic mechanism are usually inferred from a series of biochemical experiments. Here, we derive an enzyme mechanism from true atomic-resolution x-ray structures of reaction intermediates. Two ultra-high resolution structures of wild-type and mutant d-2-deoxyribose-5-phosphate (DRP) aldolase complexes with DRP at 1.05 and 1.10 angstroms unambiguously identify the postulated covalent carbinolamine and Schiff base intermediates in the aldolase mechanism. In combination with site-directed mutagenesis and (1)H nuclear magnetic resonance, we can now propose how the heretofore elusive C-2 proton abstraction step and the overall stereochemical course are accomplished. A proton relay system appears to activate a conserved active-site water that functions as the critical mediator for proton transfer. 相似文献
12.
DNA structure: evidence from electron microscopy 总被引：9，自引：0，他引：9
J D Griffith 《Science (New York, N.Y.)》1978,201(4355):525-527
The contour lengths of phiX174 DNA duplex and RNA-DNA hybrid molecules were measured by several commonly used electron microscopic techniques. The countour length of the hybrid molecules corresponds to a rise of 2.5 to 2.6 angstroms per base pair, as expected for the A conformation, while the length of phiX174 duplex DNA similarly measured corresponds to a 2.9-angstrom rise, very different from 3.4 angstroms of the classic B form. Thus any chromatin structure parameter based on electron microscopy and a rise of 3.4 angstroms must be reappraised. The possibility that DNA in dilute solution also has a rise of 2.9 angstroms and a screw of 10.5 base pairs per turn is discussed. 相似文献
13.
Oshikane H Sheppard K Fukai S Nakamura Y Ishitani R Numata T Sherrer RL Feng L Schmitt E Panvert M Blanquet S Mechulam Y Söll D Nureki O 《Science (New York, N.Y.)》2006,312(5782):1950-1954
Glutaminyl-transfer RNA (Gln-tRNA(Gln)) in archaea is synthesized in a pretranslational amidation of misacylated Glu-tRNA(Gln) by the heterodimeric Glu-tRNA(Gln) amidotransferase GatDE. Here we report the crystal structure of the Methanothermobacter thermautotrophicus GatDE complexed to tRNA(Gln) at 3.15 angstroms resolution. Biochemical analysis of GatDE and of tRNA(Gln) mutants characterized the catalytic centers for the enzyme's three reactions (glutaminase, kinase, and amidotransferase activity). A 40 angstrom-long channel for ammonia transport connects the active sites in GatD and GatE. tRNA(Gln) recognition by indirect readout based on shape complementarity of the D loop suggests an early anticodon-independent RNA-based mechanism for adding glutamine to the genetic code. 相似文献
14.
Recrystallization of the solid Cd(10)S(4)(SC(6)H(5))(12) from a solution of pyridine and N, N-di-methylformamide (DMF) results in the formation of the cluster Cd(32)S(14)(SC(6)H(5))(36)-DMF(4) as pale yellow cubes. The structure consists of an 82-atom CdS core that is a roughly spherical piece of the cubic sphalerite lattice approximately 12 angstroms in diameter. The four corners of the lattice are capped by hexagonal wurtzite-like CdS units, which results in an overall tetrahedral cluster approximately 15 angstroms in diameter. This cluster dissolves intact in tetrahydrofuran where its absorption spectrum reveals a sharp peak at 358 nanometers at room temperature and its emission spectra show a strong broad band at 500 nanometers. 相似文献
15.
ZSM-18 is the first known aluminosilicate zeolite to contain rings of three (Si,Al)-O species (3-rings). Its framework topology has been determined by hypothetical model building, subsequent constrained distance and angle least-squares refinements of atomic coordinates, and x-ray powder diffraction pattern simulations. Its channel structure is characterized by a linear unidimensional 12-ring channel, with an approximate pore opening of 7.0 angstroms. In addition, the channels are lined with pockets that are capped by 7-rings with dimensions of 2.8 angstroms by 3.5 angstroms. An intraframework packing model of the organic moiety used in the synthesis suggests that a strong templating effect may be responsible for the formation of this unusual zeolite structure. 相似文献
16.
Molecular structure of DNA by scanning tunneling microscopy 总被引：5，自引：0，他引：5
A Cricenti S Selci A C Felici R Generosi E Gori W Djaczenko G Chiarotti 《Science (New York, N.Y.)》1989,245(4923):1226-1227
Uncoated DNA molecules marked with an activated tris(l-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with the use of a high-resolution scanning tunneling microscope (STM). Constant-current and gap-modulated STM images show clear evidence of the helicity of the DNA structure: pitch periodicity ranges from 25 to 35 angstroms, whereas the average diameter is 20 angstroms. Molecular structure within a single helix turn was also observed. 相似文献
17.
Crystals of a high-pressure form of benzene (benzene 11) were grown in the diamond-anvil pressure cell at elevated temperature and pressure from the transition of solid I to solid II. X-ray precession data were obtained from a single-crystal in the high-pressure cell. At 21 degrees C and about 25 kilobars, benzene II crystallizes in the monoclinic system with a = 5.417 +/- 0.005 angstroms (S.D.), b = 5.376 +/- 0.019 angstroms, c = 7.532 +/- 0.007 angstroms, beta = 110.00 degrees +/- 0.08 degrees , space group P2(1)/ c, Pc= 1.26 grams per cubic centimeter. The crystal structure was solved by generating all possible molecular packing configurations and calculating structure factors, reliability factors, and packing energies for each configuration. This procedure produced a unique solution for the molecular packing of benzene II. 相似文献
18.
Ultrastructure of gamma-M immunoglobulin and alpha macroglobulin: electron-microscopic study 总被引：4，自引：0，他引：4
Electron microscopy of purified Waldenstr?m macroglobulins and normal human and rabbit gammaM immunoglobulins revealed spider-like structures with five legs varying in length and often joining a central ring. Usually only the central more rigid part of this structure (about 150 by 170 angstroms) was clearly visible, but occasionally particles were seen with longer very flexible legs having a total span of about 350 angstroms. Molecules of gammaM antibody retained antibody activity during preparation for electron microscopy. Human and rabbit alpha macroglobulins revealed more rigid symmetric structures (100 by 200 angstroms) which resembled the Russian letter . 相似文献
19.
Thiamine diphosphate (ThDP) is used as a cofactor in many key metabolic enzymes. We present evidence that the ThDPs in the two active sites of the E1 (EC 1.2.4.1) component of the pyruvate dehydrogenase complex communicate over a distance of 20 angstroms by reversibly shuttling a proton through an acidic tunnel in the protein. This "proton wire" permits the co-factors to serve reciprocally as general acid/base in catalysis and to switch the conformation of crucial active-site peptide loops. This synchronizes the progression of chemical events and can account for the oligomeric organization, conformational asymmetry, and "ping-pong" kinetic properties of E1 and other thiamine-dependent enzymes. 相似文献
20.
Three-dimensional structure at 0.86 A of the uncomplexed form of the transmembrane ion channel peptide gramicidin A 总被引：10，自引：0，他引：10
D A Langs 《Science (New York, N.Y.)》1988,241(4862):188-191
The crystal structure of the uncomplexed orthorhombic form of gramicidin A has been determined at 120 K and at 0.86 angstrom resolution. The pentadecapeptide crystallizes as a left-handed antiparallel double-stranded helical dimer with 5.6 amino acid residues per turn. The helix has an overall length of 31 angstroms and an average inner channel diameter of 4.80 angstroms. The channel of this crystalline form is void of ions or solvent molecules. The channel diameter varies from a minimum of 3.85 angstroms to a maximum of 5.47 angstroms and contains three pockets where the cross-channel contacts are 5.25 angstroms or greater. The range of variation seen for the phi and psi torsion angles of the backbone of the helix suggests that these potential ion binding sites can be induced to travel the length of the channel in a peristaltic manner by cooperatively varying these angles. The indole rings of the eight tryptophan residues of the dimer are overlapped in three separate regions on the outer surface of the helix when viewed down the barrel of the channel. This arrangement would permit long-chained lipid molecules to nest parallel to the outer channel surface between these protruding tryptophan regions and act like molecular splines to constrain helical twist deformations of the channel. 相似文献