Acta Crystallographica Section D: Biological Crystallography最新文献

{"title":"Present at the Flood. By Richard E. Dickerson. Sunderland, Mass.: Sinauer Associates, Inc., 2005. Pp. 307. Price (paperback) US$ 36.95. ISBN 0-87893-168-6.","authors":"W. Hunter","doi":"10.1107/S0907444907013558","DOIUrl":"https://doi.org/10.1107/S0907444907013558","url":null,"abstract":"First you should know something of the author. Richard ‘Dick’ Dickerson was a participant in some of the early computational crystallography on myoglobin whilst a post-doc in Cambridge. This, when a significant amount of the world wide available computing resource was devoted to crystallographic calculations, was adventurous. The successful experience and now knowing the difference between protons and proteins set him on the career path during which he has investigated the structural biology of cytochrome proteins and their molecular evolution, protein–nucleic acid associations and perhaps the work with which he is most closely associated, the intricacies of DNA structure and interactions with drugs. So, with his credentials established for the younger readers, let us begin. Dick Dickerson identifies the period between 1933 and 1963 as the genesis of structural molecular biology. He then tells the story of how protein structure came to be investigated by fibre diffraction, and modelled and then how the models could be tested. How DNA came into the limelight and of the race to produce the correct model of this macromolecule. Of how single crystal diffraction methods progressed and eventually revealed the structures of myoglobin and hemoglobin. And then of how, following a period of consolidation (drought) the field of structural biology took off. Perhaps this sounds like a nice little book reviewing an interesting period in science. It most certainly is not. This is a book about important science and real people who shaped a cornerstone of modern biological, chemical and biomedical research. We often take things for granted especially in our science, as progress appears relentless. There is a risk that in our diet of facts the methods and reasoning, occasional serendipity and fate, that allowed to us obtain the facts in the first place are lost. Often, in the dryness of a scientific publication, where all aspects are clearly laid out and explained, what is missing is the sometimes chaotic reality of how and why things actually happened. What factors influenced decisions? So, with respect to structural biology some of the answers are to be found here as Dick takes us on a journey that evolves from Astbury working in Leeds, down to Kings College in London and up to Cambridge, and across the Atlantic a couple of times. The story involves a sickbed in Oxford, slabs of whale meat, conferences organised to coincide with good skiing in Austria, the speed of an owls blink, arson and sinister McCarthyism. The story encompasses chemistry, physics and biology with a little bit of politics and sociology mixed in. Human strengths are evident and some frailties are exposed; as in every aspect of life these can determine success or failure and often how contributions are remembered. The author’s admiration for the many of the contributors to the story shines through. There are no villains but there are examples of arrogance, ignorance, at least one ‘monstrous eg","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2007-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77464056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PET Chemistry. The Driving Force in Molecular Imaging. Edited by P. A. Schubiger, L. Lehmann & M. Friebe. Pp. xii + 339. Berlin: Springer-Verlag, 2007. Price (hardback) Euro 88.76. ISBN-103-540-32623-5.","authors":"P. Paufler","doi":"10.1107/S0907444906056113","DOIUrl":"https://doi.org/10.1107/S0907444906056113","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2007-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79696275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SPINE: Structural Proteomics in Europe - The best of both worlds","authors":"D. Stuart, E. Jones, K. Wilson, S. Daenke","doi":"10.1107/S0907444906035347","DOIUrl":"https://doi.org/10.1107/S0907444906035347","url":null,"abstract":"Division of Structural Biology, University of Oxford, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, England, and York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, England The concept of structural genomics arose in the mid to late 1990s in the USA and Japan as a response to the success of high-throughput (HTP) sequencing methods applied to whole genomes (see http://www.isgo.org). It was imagined that similar HTP methods could be applied to obtain three-dimensional structures of all the proteins (the ‘proteome’) of an organism, which would in particular be an efficient way of filling in the gaps in observed ‘fold-space’. This vision led to the investment of substantial sums of money into large-scale structural genomics projects in the USA [e.g. nine projects funded by the NIH/NIGMS Protein Structure Initiative (PSI) from September 2000 to June 2005, http://www.nigms.nih.gov/psi/] and Japan (e.g. the massive RIKEN project, http:// www.rsgi.riken.go.jp/). These were characterized by the concentration of resources into a small number of large centres, the development of novel, automated technologies to permit a HTP pipeline approach to structure determination, and a focus on novel folds as the major target criteria. The US-based projects, in addition, required immediate public deposition of structural data whereas the Japanese RIKEN project also aimed to support Japanese industry, precluding deposition in advance of patent evaluation. Europe was slower in implementing HTP approaches to structural biology. The Protein Structure Factory in Berlin, Germany (http://www.proteinstrukturfabrik.de/) led the way, followed by the Oxford Protein Production Facility (OPPF) in Oxford, UK (http:// www.oppf.ox.ac.uk/) and the Genopoles in France (notably Gif, Marseille and Strasbourg, http://rng.cnrg.fr/). However, it was not until October 2002 that the first Europe-wide project began. This was a three-year project funded by the EU FP5 programme called SPINE: Structural Proteomics IN Europe (http://www.spineurope.org). SPINE, a ‘second generation’ structural genomics project (indeed purposefully called a Structural Proteomics project to draw a distinction), made some radical departures from the firstgeneration initiatives, while at the same time obviously benefiting from the experience and technology development of the preceding projects. The challenge set for SPINE was to push forward with cutting-edge technologies aimed at biomedically relevant targets at the same time as generating a pan-European integration on biomedically focused structural proteomics. The SPINE consortium comprised","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2006-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91017200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Get-Phases Beijing 2005","authors":"Xiaodan Su, T. Terwilliger","doi":"10.1107/S0907444906024759","DOIUrl":"https://doi.org/10.1107/S0907444906024759","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2006-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76928217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Low-resolution ab initio phasing of Sarcocystis muris lectin SML-2.","authors":"Jürgen J. Müller, N. Lunina, A. Urzhumtsev, E. Weckert, U. Heinemann, V. Lunin","doi":"10.1107/S0108767306095158","DOIUrl":"https://doi.org/10.1107/S0108767306095158","url":null,"abstract":"Structural analysis of the lectin SML-2 faced difficulties when applying standard crystallographic phasing methods. The connectivity-based ab initio phasing method allowed the computation of a 16 A resolution Fourier synthesis and the derivation of primary structural information. It was found that SML-2 crystals have three dimers in the asymmetric part of the unit cell linked by a noncrystallographic symmetry close to translation by (0, 0, 1/3). A clear identification of the noncrystallographic twofold axis explains the space-group transformation from the primitive P2(1)2(1)2(1) to the C-centred C222(1) observed during annealing procedures within an N(2) cryostream for cocrystals of SML-2 and galactose. Related packing considerations predict a possible arrangement of SML-2 molecules in a tetragonal unit cell. Multiple noncrystallographic symmetries and crystal forms provide a basis for further image improvements.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2006-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75637603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biofunctionalization of Nanomaterials. Edited by Challa Kumar. Nanotechnologies for Life Sciences. Volume 1. Pp. xx+366. Weinheim: Wiley–VCH Verlag GmbH Co. KGaA, 2005. Price (hardcover) 139 Euro/220 SFR. ISBN: 3-527-31381-8","authors":"W. Pompe","doi":"10.1107/S0907444906008729","DOIUrl":"https://doi.org/10.1107/S0907444906008729","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2006-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80375624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure of the novel alpha-amylase AmyC from Thermotoga maritima.","authors":"A. Dickmanns, M. Ballschmiter, W. Liebl, R. Ficner","doi":"10.2210/pdb2b5d/pdb","DOIUrl":"https://doi.org/10.2210/pdb2b5d/pdb","url":null,"abstract":"alpha-Amylases are essential enzymes in alpha-glucan metabolism and catalyse the hydrolysis of long sugar polymers such as amylose and starch. The crystal structure of a previously unidentified amylase (AmyC) from the hyperthermophilic organism Thermotoga maritima was determined at 2.2 Angstroms resolution by means of MAD. AmyC lacks sequence similarity to canonical alpha-amylases, which belong to glycosyl hydrolase families 13, 70 and 77, but exhibits significant similarity to a group of as yet uncharacterized proteins in COG1543 and is related to glycerol hydrolase family 57 (GH-57). AmyC reveals features that are characteristic of alpha-amylases, such as a distorted TIM-barrel structure formed by seven beta-strands and alpha-helices (domain A), and two additional but less well conserved domains. The latter are domain B, which contains three helices inserted in the TIM-barrel after beta-sheet 2, and domain C, a five-helix region at the C-terminus. Interestingly, despite moderate sequence homology, structure comparison revealed significant similarities to a member of GH-57 with known three-dimensional structure, Thermococcus litoralis 4-glucanotransferase, and an even higher similarity to a structure of an enzyme of unknown function from Thermus thermophilus.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2006-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85952001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure Determination by X-ray Crystallography. By Mark Ladd and Rex Palmer. Pp. xlii + 819. New York: Kluwer Academic/Plenum Publishers, 4th ed., 2003. Price (paperback) GBP 41. ISBN 0-306-47454-9.","authors":"J. Helliwell","doi":"10.1107/S0907444906002010","DOIUrl":"https://doi.org/10.1107/S0907444906002010","url":null,"abstract":"I was very surprised when I was asked by the Editors to write a book review of this Fourth Edition to find that there was no book review for the former editions in the IUCr journals, since ‘Ladd & Palmer’ is a very famous and fundamental book on the subject of crystal structure determination. Therefore, I accepted to write the review, although this edition was published about three years ago. Currently, intensity data are collected automatically within two or three hours using a diffractometer with a twodimensional detector, and the crystal structure can be solved automatically using a convenient software package. The crystal and molecular structures will be drawn on the display of the personal computer. Moreover, all of the crystallographic data and the details of the structure determination are formatted in a crystallographic information file (CIF). It may be possible to submit a report of the crystal structure analysis without any knowledge of crystallography. However, the number of such ideal crystals whose structures are determined automatically is gradually decreasing. We must often analyze the structures of twinned crystals and crystals with disordered groups, solvate molecules or false symmetry. Deep knowledge of crystallography is necessary to overcome such difficult problems. This book is well adapted not only for the beginner but also for the researcher if they want to know the basis of crystallography. In addition to basic crystallography, the following three chapters were added in this edition: X-ray Structure Determination with Powders (chapter 9); Proteins and Macromolecular X-ray Analysis (chapter 10); and Computer-Aided Crystallography (chapter 11). Recently the structure determination of organic and macromolecules using powder diffraction data has been extensively developed. In addition to an explanation of the methods of data collection, indexing and the assignment of the unit cell and space group, an outline of how to build the model structure is described. Not only the reciprocalspace method but also the several directspace methods are explained in detail. Several examples analyzed by powder diffraction are shown. There are many books on protein crystallography. However, I think it is adequate, as the authors suggest in chapter 10, that, although there are definite distinctions between large and small molecules in the crystallographic arena, there is no reason to exclude one from the other, and that there are many advantages of being familiar with both. The chapter includes the methods of crystallization, data collection and processing, phase determination using isomorphous replacement, molecular replacement and multiple-wavelength anomalous dispersion, and structure refinement such as density modification, simulated annealing and least-squares methods. Computing is an essential feature in any modern crystallographic investigation. The basic computation programs for singlecrystal and powder structure determinations are explai","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2006-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82904661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The integration of macromolecular diffraction data.","authors":"A. Leslie","doi":"10.1107/97809553602060000675","DOIUrl":"https://doi.org/10.1107/97809553602060000675","url":null,"abstract":"The objective of any modern data-processing program is to produce from a set of diffraction images a set of indices (hkls) with their associated intensities (and estimates of their uncertainties), together with an accurate estimate of the crystal unit-cell parameters. This procedure should not only be reliable, but should involve an absolute minimum of user intervention. The process can be conveniently divided into three stages. The first (autoindexing) determines the unit-cell parameters and the orientation of the crystal. The unit-cell parameters may indicate the likely Laue group of the crystal. The second step is to refine the initial estimate of the unit-cell parameters and also the crystal mosaicity using a procedure known as post-refinement. The third step is to integrate the images, which consists of predicting the positions of the Bragg reflections on each image and obtaining an estimate of the intensity of each reflection and its uncertainty. This is carried out while simultaneously refining various detector and crystal parameters. Basic features of the algorithms employed for each of these three separate steps are described, principally with reference to the program MOSFLM.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85340660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Data collection and analysis","authors":"G. Evans, M. A. Walsh","doi":"10.1107/S0907444905040631","DOIUrl":"https://doi.org/10.1107/S0907444905040631","url":null,"abstract":"In this chapter, I present methodological aspects related to data collection and analysis. I present data sources within each case including detailed information with regard to interviewee characteristics. The data collection approach differs between the pilot Case A and the four follow up Cases B‐E. In consequence, I present the longitudinal data collection approach of the pilot case first and continue with the data collection at Cases B‐E. I end with a description of data analysis procedures.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78488142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}