... perfection of part and adequacy of collection In this book the use of ``program'' is focused on the creation, execution, and study ofprograms written in a dialect of Lisp for execution on a digital computer ... matter of this book involves us with three foci of phenomena: the human mind, collections ofcomputer programs, and the computer Every computer program is a model, hatched in the mind, of a real ... Poorly-Understood and Sloppily-Formulated Ideas'' ``The StructureandInterpretationofComputerPrograms' ' is the entry-level subject in computer science at the Massachusetts Institute of Technology...
... examination of the structureand function ofcomputer hard drives and DNA Theoretical Biology and Medical Modelling 2010 7:3 Submit your next manuscript to BioMed Central and take full advantage of: ... description of the informational and computational elements of a cell and the architecture of a computer system [1,2] Since the cell represents a level of complexity that is orders of magnitude ... mappings in terms of organization andstructure A central common feature of both cellular and silicon systems is the existence of a dedicated and distinct centralized information storage and processing...
... implications of the cycle of histone acetylation and deacetylation that accompanies cycles of transcription, and highlight the special significance of histone H4 lysine 16 acetylation Active chromatin and ... functions of PARP-1 are activated in the presence of NAD+ it mediates the PARylation of both histones and PARP-1 itself, and thereby promotes decondensation of higher order chromatin structure ... with binding of both MOF and Tip60 (equivalent to Esa1 in yeast NuA4) [124,130] However, in human cells depletion of MOF, but not Tip60, results in reduced global levels of AcH4-K16 and defective...
... domains of Spir-2 and PTPN13 were generated by RT-PCR and inserted into pEGFP-C1 and pGEX-4T-2 The N- and C-terminal regions of the v-KIND KIND2 and the MAP2 CD were generated by PCR and cloned ... series of GST-fused deletions of the CD2-1 region (Fig 3E) and examined the interactions between bacterially expressed proteins of these subregions (Fig S1C) and 1654 Fig Of all members of the ... in dendrites of cultured hippocampal neurons Fig S4 Domain structureof MAP2 and the alignment of v-KIND-binding core (BD) region of MAP2 CD2 domain (702–744 aa) in human, mouse and Gallus This...
... patterns and processes at different levels of biological organization: from the life histories of individuals, to the structureand dynamics of populations and communities, to the fluxes and pools of ... measuring and understanding the roles of different kinds of organisms in the flux and storage of elements in ecosystems The total biomass per unit area, W, is simply the sum of the body mass of all ... abundances and turnover of populations, the allocation of resources among coexisting species, and the fluxes and pools of energy and materials in ecosystems These exchanges are direct consequences of...
... representation of the structureof the PSI domain of barley prophytepsin [25] (N-terminal domain, blue; C-terminal domain, red) (C) Model structureof the PSI domain of cardosin A based on the crystal structure ... by the prosegment, but also by the 13 residues of the N-terminal of the mature enzyme and by the ÔflapÕ The anchorage of the prosegment andof part of the N-terminus in the active site cleft is ... isoforms by the excision of the prosegment andof most of the PSI [21] Conversely to what has been found in vivo [31], heavy and light chains of the processed forms of recombinant cyprosin are...
... analysis of the DNA of different Conus species has already revealed a large number of a-conotoxin sequences [45] and the identification of further specific nAChR ligands is likely The advantage of a ... consisting of the extracellular ligand-binding domain of the a6 subunit and the transmembrane and intracellular domains of the a3 subunit was used in this study PIA selectively blocks rat and human ... determination of the subunit composition of the nAChRs involved has been hindered by the lack of selective ligands and imperfect correlations between the characteristics of native and heterologously...
... the structureand PDB code shown below each panel (A) Overlap of isoform 337 with the structureof the longer isoform CfAFP-501 using the main chain of residues Thr23fiAsn90 in isoform 337 and ... other and with proteins that have a similar fold Structureof sbwAFP and TmAFP The structureof sbwAFP has been determined by X-ray ˚ crystallography to 2.5 A and by NMR at both 30 °C and °C ... method and PDB code shown below each panel (A) Overlap of X-ray structure with °C NMR structure using the main chain of residues Ser12fiThr70 in the structure alignment (B) Overlap of the X-ray structure...
... hemocyanin of which the complete molecular structure is known This allows us to compare structure, and intra- and intermolecular evolution of hemocyanins from Myriapoda, Crustacea and Chelicerata ... composed of 12 HcA, 12 HcB, six HcC and six HcD polypeptides Thus the basic building block of the hemocyanin, the hexamer, most likely contains two copies of each HcA and HcB, and single copies of ... data analyses and phylogenetic studies The tools provided with Genetics Computer Group (GCG) Software Package 10 and by the ExPASy Molecular Biology Server of the Swiss Institute of Bioinformatics...
... longer-chain (and nonglobular) versions of the structureof the Bowman±Birk inhibitor in Fig The X-ray crystal structure pi2 reveals that the /,w angles of most of the residues of the Bowman±Birk ... form of b strand [18] The positive bands at » 1675 cm)1 in the amide I region of the ROA spectra of b- and j-casein, which originate mainly in the peptide C O stretch, are characteristic of disordered ... attribute the lack of agreement between our present results and the earlier interpretations of the UVCD spectra of b- and j-caseins (see above) to the fact that the basis sets of protein UVCD spectra...
... study of problem solving action and report: I) the collected of data on problem solving and talk about problem solving, 2) development of a process model of these behaviors, and 3) use of coding ... problem solving from a record of the problem solving report and a record of moves made Then, we use this extracted trace to evaluate our model of the role of point of view in problem solving SUMMARY ... organization of the problem ("point of view"), and systematic multl-utterance structures used to express the forms of inference used to solve the problem ("Justificatlon argument structures")...
... essential for defining precise specifications of what programs Like StructureandInterpretationofComputer Programs, by Abelson, Sussman, & Sussman [1, 2], our book mostly uses the computation-based ... inside computer systems Modern computers are highly complex systems consisting of hardware, operating system, middleware, and application layers, each of which is based on the work of thousands of ... settings of their alarm clock or cellular phone) and specialists (computer programmers, the audience of this book) This book focuses on the construction of software systems In that setting, programming...
... and fD are the mass fractions of monomer and dimer, respectively, and RgM and RgD are the radii of gyration for the monomer and dimer, respectively Missing pieces of crystallographic models were ... 1) Radius of gyration, model fitting and analysis For a mixture of monomeric and dimeric scattering species, the radius of gyration is given by: R2 ¼ fM R2 þ fD R2 g gM gD ð7Þ where fM and fD are ... scattering of monomeric arrestin, the forward scattering from a mixture of monomers and dimers is: Ið0ÞTotal ¼ fM Ið0ÞM þ 2fD Ið0ÞM ð1Þ where fM and fD are the mass fractions of monomer and dimer,...
... solution structureof the C-domain (A) Stereo view of the ensemble of the final 48 calculated structures Twenty-four structures of the closed protein conformer are shown in red, and 24 structures of ... of eRF1 Fig S11 The Ramachandran map plot (/ and w torsion angles for the protein backbone) of all 24 conformers of the NMR families of solution structures of the closed and open conformers of ... structure calculation for the open and closed conformers of the C-terminal domain of human eRF1 Fig S3 NOE map of the minidomain (residues 329– 372) of human eRF1 NMR structureand function of...
... the apo structureof S aureus EF-G Overall structureand comparison with previous EF-G structures All five domains of S aureus EF-G are ordered in our structure The overall conformation of the ... helices AV and BV at the surface of domain V Gly621 and Gly617 are in the area of contact with the 1095 and 2473 regions of 23S RNA The two helices are facing the ribosome, and the four-stranded b-sheet ... thermophilus EF-G structures, wild type and various mutants, domains III, IV and V display a movement relative to domains I and II, resulting in a shift of the ˚ tip of domain IV of up to A [14,16]...
... identification and distribution of TLP genes in nature, the structural and functional characterization of the TLP from various organisms, and the evolution of TLP and transthyretin The identification of TLPs ... structures of these proteins, all tetrameric, showed significant similarity to the published structures of transthyretin By way of example, a comparison of the structureof S dublin TLP with the structures ... in TLP structures as a result of alterations to the formation of hydrogen bonds between strands The carbonyls of residues V104 and P105 (zebrafish TLP numbering), in the middle of b-strand G,...
... comparison of part of the protein backbone structureof the representative solution structureof the human eRF1 M domain and the Ca trace in the crystal structureof RF1 in the whole ribosome structure ... pairwise superimposition of five-residue segments of the crystal structure on the equivalent segments of each member of the family of the solution structureof the M domain of human eRF1 The resulting ... crystal structureof the M domain of the human eRF1 [3] is superimposed on the same set of atoms in the representative solution structureand is shown in red (B) The topology of the M domain of human...
... to PLP and not mobile (Fig 5), although it participates in the induced fit (Fig 4) The mobility distributions of CysM(K268A), wildtype CysM and CysM(salmo), and those of subunits B and D of CysM(RKE), ... 2007 FEBS 5383 Structureof the O-acetylserine sulfhydrylase CysM G Zocher et al Fig Stereo ribbon plot of the high resolution structureof the CysM dimer, including the molecular twofold axis (black), ... defines the thiol position of TNB to a small region above the plane of the acrylate double bond As a result of this constraint andof the spacious active center pocket of CysM, TNB was placed rather...
... in which the b1-strand and b2-strand are adjacent and parallel to each other, and the b¢-strand is adjacent and antiparallel to the b1-strand (Fig 1) The length and sequence of the variable loop ... Valverde et al Structureand function of KH domains A B C Fig 10 Crystal structureof tandem type II KH domains of NusA in complex with RNA The tandem KH1–KH2 domains of NusA recognize RNA ligand 5¢-GAACUCAAUAG ... comparison is limited, however, because the structureof only one of each type of tandem KH domain has been published Here we compare the structures of the tandem KH1–KH2 domains from protein NusA...