Acta Crystallographica Section D: Biological Crystallography最新文献_第9页

Protein-Ligand Interactions: Methods and Applications. Edited by G. U. Nienhaus. Pp. xi + 568. Totowa, New Jersey: Humana Press, 2005. Price (hardback) GBP 87.45, USD 135.00. ISBN 1-58829-372-6.

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2005-10-01 DOI: 10.1107/S0907444905029410

L. Sawyer

{"title":"Protein-Ligand Interactions: Methods and Applications. Edited by G. U. Nienhaus. Pp. xi + 568. Totowa, New Jersey: Humana Press, 2005. Price (hardback) GBP 87.45, USD 135.00. ISBN 1-58829-372-6.","authors":"L. Sawyer","doi":"10.1107/S0907444905029410","DOIUrl":"https://doi.org/10.1107/S0907444905029410","url":null,"abstract":"Since the elucidation of the human genome, and to some extent even before that, the problem of divining the function of a protein given only its amino-acid sequence has been exercising biochemists. With the various post-genomic initiatives to determine the three-dimensional structures of all of the gene products in a given genome, the problem has become ever more pressing – given the structure of a protein, how do you find out what it does? One way is to try to identify the physiologically important molecules with which it interacts in the hope that vital functional clues will emerge. Thus, a wide selection of methods that can be applied to give binding information is essential if the wide differences in structure, solubility and function of ligand and protein are to be accommodated. An additional benefit of this methodology is in the search for new drugs. The book Protein–Ligand Interactions, one in the Methods in Molecular Biology series, sets out a variety of such methods, some well established, others quite new, by which the interactions of proteins with their ligands can be investigated. The 24 chapters, each written by experts in their technique, cover a wide range of methods from the ’wet’ through the biophysical to the computational. While several of the methods will be familiar to most, a few are quite new, or at least their application to biological systems is novel. The general approach, however, of each chapter is the same: a summary, a general introduction explaining the basic principles of the method and the types of problem that can be tackled, the materials and the instrumentation to be used in some typical experiments, which are then described and the results are shown and discussed. Each chapter ends with notes that amplify points made in the body of the text, and of course, an up-to-date reference list. For the established methods, reference to the seminal early literature is also to be found. Several of the chapters cover methods appropriate for the time-resolution of the interaction, necessary to examine intermediate states along a reaction pathway. Thus, chapters on X-ray crystallography, IR, Raman and fluorescence techniques deal with binding to haem proteins, GTPases and lysozyme. High-throughput methods are now seen as essential to the pharmaceutical industry if not elsewhere, but only one chapter deals with a fluorescence screening method based around confocal microscopy such that 1536 different binding experiments carried out in 5 ml drops can be monitored in about half an hour. One aim of this method development is to reduce still further the sample volumes and hence total amounts of both protein and ligand required to provide evidence of binding. It is perhaps to the more unusual methods, however, that many will turn. There is a fascinating chapter on the use of single-molecule fluorescence that detects the conformational fluctuations associated with ligand binding. Equally intriguing is the use of atomic force micros","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2005-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79280550","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}

引用次数: 2

Parameter-space screening: a powerful tool for high-throughput crystal structure determination. Corrigendum 参数空间筛选:高通量晶体结构测定的有力工具。应改正的错误

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2005-09-01 DOI: 10.1107/S0907444905024996

Zhi-jie Liu, Dawei Lin, W. Tempel, Jeremy L. Praissman, J. Rose, Bi-Cheng Wang

引用次数: 1

Escherichia coli MltA: MAD phasing and refinement of a tetartohedrally twinned protein crystal structure (vol D61, pg 613, 2005) 大肠杆菌MltA:四面体双生蛋白晶体结构的MAD相位和细化(vol D61, pg 613, 2005)

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2005-08-01 DOI: 10.1107/S0907444905013533

T. Barends, R. D. Jong, K. Straaten, A. Thunnissen, B. Dijkstra

引用次数: 0

Redefining Acta D 重新定义学报D

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Acta Crystallographica Section D: Biological Crystallography Pub Date : 2005-01-01 DOI: 10.1107/S0907444904032548

E. Baker, Z. Dauter

引用次数: 1

Model building and refinement 模型构建和细化

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Acta Crystallographica Section D: Biological Crystallography Pub Date : 2004-12-01 DOI: 10.1107/S0907444904028586

M. Noble, A. Perrakis

引用次数: 0

Crystallization and preliminary X-ray analysis of GlcNAc alpha 1,4Gal-releasing endo-beta-galactosidase from Clostridium perfringens. 产气荚膜梭菌GlcNAc α 1,4gal释放内切-半乳糖苷酶的结晶及x射线初步分析

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2004-11-25 DOI: 10.2210/pdb1ups/pdb

Lu Deng, Zhi-jie Liu, H. Ashida, Su-chen Li, Yu-Teh Li, P. Horanyi, W. Tempel, J. Rose, Bi-Cheng Wang

引用次数: 1

David Mervyn Blow: a scholar and a gentleman (1931–2004) 大卫·默文·布罗:学者和绅士(1931-2004)

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2004-10-01 DOI: 10.1107/S0907444904018384

B. Matthews

{"title":"David Mervyn Blow: a scholar and a gentleman (1931–2004)","authors":"B. Matthews","doi":"10.1107/S0907444904018384","DOIUrl":"https://doi.org/10.1107/S0907444904018384","url":null,"abstract":"My association with David Blow (photograph ca 1967), which was a pivotal step in my career, was due more to good luck than good management. As a PhD student in Australia working in`small molecule' crystallography, I had written to Max Perutz asking about the possibility of doing postdoctoral work in his laboratory and was very excited to be accepted. My wife and I arrived in Cambridge in November 1963, the same week that President Kennedy had been assassinated. The Union Jack over the Medical Research Council laboratory was ¯ying at half-mast, an extraordinarily rare sign of respect under any circumstances, let alone for a non-citizen. When I introduced myself to Perutz he indicated that, since we had ®rst corresponded, two other postdoctoral associates had already joined his group. If I still wanted to work with him I would be free to do so, he said, but at the same time he strongly urged me to consider the possibility of joining another group within the MRC laboratory. David Blow's group was one such possibility. I was aware that David had several publications in protein crystallography but the only article of his that I had read with any care was the notèTo ®t a plane to a set of points by least squares'. It is possibly his least-quoted publication but one which was relevant to my thesis project. I was, however, immediately taken with David's personality and sensed that we would get on well together. Furthermore, Michael Rossmann, who had been David's long-standing collaborator, was about to assume a new position at Purdue University. Also his technician, Barbara Jeffery, was about to move to the Boston area. I had little hesitation in joining David's group. Paul Sigler was to join six months later, technically as a PhD student although with substantial prior experience in David Davies' laboratory and as a practising MD","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2004-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79320137","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}

引用次数: 0

Carl-Ivar Brändén (1934–2004)

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2004-09-01 DOI: 10.1107/S0907444904018189

Jane Smith

{"title":"Carl-Ivar Brändén (1934–2004)","authors":"Jane Smith","doi":"10.1107/S0907444904018189","DOIUrl":"https://doi.org/10.1107/S0907444904018189","url":null,"abstract":"Science lost a valued citizen on 28 April 2004 when Carl-Ivar BraÈndeÂn succumbed to lung cancer following an 18-month battle. BraÈndeÂn was a prominent member of the structural biology community. Carl grew up in Lapland in northern Sweden, where his father was the teacher in a one-room schoolhouse. His active and free childhood instilled a life-long love of exploration and nature. At the same time he developed a strong desire to expand his horizons beyond the frozen north, and decided that a good education was his ticket to rest of the world. This led him, from age 13 onward, to schooling away from his family and eventually to Uppsala University. Carl's higher education in science was characterized by an ability to take opportunities where and when he found them and by an intellect that was restless unless challenged with an important problem. He began studying mathematics and physics at Uppsala University, but, bored by the undergraduate physics curriculum and inspired by Linus Pauling's texts, he switched to chemistry. An early and important mentor was Professor Ingvar Lindqvist, who invited Carl into his laboratory for PhD studies in chemical crystallography. During his studies with Lindqvist, Carl co-authored a least-squares re®nement program for the ®rst Swedish electronic computer and used it to re®ne the structures of several metal coordination complexes he had solved. Again bored and on the verge of leaving both crystallography and chemistry, Carl was enticed to the new ®eld of protein crystallography by a lecture course in biochemistry. Thus, he leapt at a postdoctoral opportunity to develop re®nement methods for myoglobin with John Kendrew at the MRC laboratory in Cambridge, UK, where in 1962 joined the ®rst generation of protein crystallographers. In the company of Max Perutz, John Kendrew, Francis Crick, Fred Sanger, Michael Rossmann, David Blow, Sydney Brenner, Aaron Klug, Lubert Stryer, Richard Henderson and many others, Carl experienced the heady early days of molecular and structural biology and celebrated the Nobel prizes to Crick, Watson and Wilkins, and to Perutz and Kendrew.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2004-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78849431","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}

引用次数: 0

Structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form): a switching of partners of the sheared G.A pairs to form a functional G.AxA.G crossing. d(GCGAAGC)和d(GCGAAAGC)(四角形)的结构:剪切G.A对的伙伴交换，形成功能的G.AxA.G交叉。

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2004-04-01 DOI: 10.1107/S0907444904005104

T. Sunami, J. Kondo, I. Hirao, Kimitsuna Watanabe, K. Miura, A. Takénaka

{"title":"Structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form): a switching of partners of the sheared G.A pairs to form a functional G.AxA.G crossing.","authors":"T. Sunami, J. Kondo, I. Hirao, Kimitsuna Watanabe, K. Miura, A. Takénaka","doi":"10.1107/S0907444904005104","DOIUrl":"https://doi.org/10.1107/S0907444904005104","url":null,"abstract":"The DNA fragments d(GCGAAGC) and d(GCGAAAGC) are known to exhibit several extraordinary properties. Their crystal structures have been determined at 1.6 and 1.65 A resolution, respectively. Two heptamers aligned in an antiparallel fashion associate to form a duplex having molecular twofold symmetry. In the crystallographic asymmetric unit, there are three structurally identical duplexes. At both ends of each duplex, two Watson-Crick G.C pairs constitute the stem regions. In the central part, two sheared G.A pairs are crossed and stacked on each other, so that the stacked two guanine bases of the G.AxA.G crossing expose their Watson-Crick and major-groove sites into solvent, suggesting a functional role. The adenine moieties of the A(5) residues are inside the duplex, wedged between the A(4) and G(6) residues, but there are no partners for interactions. To close the open space on the counter strand, the duplex is strongly bent. In the asymmetric unit of the d(GCGAAAGC) crystal (tetragonal form), there is only one octamer chain. However, the two chains related by the crystallographic twofold symmetry associate to form an antiparallel duplex, similar to the base-intercalated duplex found in the hexagonal crystal form of the octamer. It is interesting to note that the significant difference between the present bulge-in structure of d(GCGAAGC) and the base-intercalated duplex of d(GCGAAAGC) can be ascribed to a switching of partners of the sheared G.A pairs.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2004-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89928391","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}

引用次数: 15

Metal-substituted derivatives of the rubredoxin from Clostridium pasteurianum. 巴氏梭菌红霉素的金属取代衍生物。

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2004-04-01 DOI: 10.1107/S0907444904004998

M. Maher, Maddalena Cross, M. Wilce, J. Guss, A. G. Wedd

引用次数: 13