Macromolecular Crystallography

A recent survey in a crystallography newsletter** Crystallography Times, a monthly eNewsletter from Rigaku Corporation, Sept. 23, 2015 edition. stated, “In the good old days, researchers had to travel to the synchrotron to collect data and stay up all night at the beamline…. The synchrotron trip was considered a right of passage to becoming a full-fledged crystallographer. Today, with FedEx crystallography, most students never visit a synchrotron. Is this a good thing or a bad thing?” And two of the possible answers were: “The all night synchrotron runs separated the wheat from the chaff and were a valuable way for PIs to discover which students were really serious,” and “People who miss the ‘good old days’ need to retire.” Although meant to be humorous, this survey captures a very real change in the last decade in both the technique of protein crystallography and the attitudes about the experiment.     

The Evolution of High-Throughput Macromolecular Crystallography at Synchrotrons

On May 11 and 12, 2000, the Stanford Synchrotron Radiation Laboratory, as it was then known, hosted a “Workshop on Techniques for Automated Mounting, Viewing and Centering Pre-Cooled Protein Crystals” [1 http://www-ssrl.slac.stanford.edu/conferences/workshops/px-robotics/. [Google Scholar], 2 E. Abola, Nature Structural Biology 7, 973–977 (2000).[Crossref], [PubMed] , [Google Scholar]]. The 12 presentations during the meeting all focused on the impact that automation could have on the performance of synchrotron beamlines and thus on research in structural biology. Two principal themes ran through the workshop: (1) robotics to mount crystals on a diffractometer; and (2) methods to place a crystal in the X-ray beam. Five conceptual and prototype robotic systems for automated mounting were described—the original ACTOR from Abbott Laboratories, later modified and marketed by Rigaku/MSC, and the systems which in final form become the ALS [3 G. Snell, Structure 12, 537–545 (2004).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]], EMBL/ESRF SC3 [4 F. Cipriani, Acta Cryst. D62(10), 1251–1259 (2006). [Google Scholar]], APS/SBC [5 D. Shu, AIP Conference Proceedings 705(1), 1201–1204 (2004).[Crossref] , [Google Scholar]], and SSRL SAM robots [6 A. E. Cohen, J. Appl. Cryst. 5(6), 720–726 (2002).[Crossref], [Web of Science ®] , [Google Scholar]]. By December of that year, the ACTOR had been installed for testing at Sector 32 of the Advanced Photon Source (Figure 1). Within three years, by the end of 2003, several of these robots, plus the commercial MARcsc from MAR Research, had been deployed to handle frozen protein crystals at beamlines for macromolecular crystallography (MX). Currently, at least 13 distinct robot types, not including variants of the ALS automounter, are employed at synchrotron beamlines to transfer crystals from storage to beam position.     

The New Macromolecular Femtosecond Crystallography (MFX) Instrument at LCLS

Macromolecular X-ray crystallography has developed, since its first use over 50 years ago to solve the structure of myoglobin, into a widely used method with broad impact in biological sciences and in society. It is today the primary technique used to obtain structural information on biomolecules that can shed light on their function and this information is often used in biomedical applications such as drug design. As this article is written, the Protein Data Bank [1 F.C. Bernstein, Journal of Molecular Biology 112(3), 535–542 (1977).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]] has just reached the milestone of 100,000 deposited X-ray structures, with a continuing trend for an ever-increasing number of structures every year. The primary contribution to this success and the increasing number of X-ray structures is the broad availability of synchrotron radiation sources with many dedicated beamlines around the world providing rapid and efficient data collection along with standard data analysis tools capable of fast data interpretation.     

Technical Report: Recent Major Improvements to the ALS Sector 5 Macromolecular Crystallography Beamlines

In a project originally aimed at X-ray proximity lithography (XRL) for semiconductor manufacturing and funded by A?STAR (Agency for Science, Technology and Research, previously National Science and Technology Board (NSTB)) and Ministry of Education (MoE), the National University of Singapore (NUS) erected SSLS building (Figure 1a) and contracted Oxford Instruments (UK) to install their Helios 2 accelerator system in 2000.     

集簇性DNA损伤在辐射研究中的进展

高LET重离子引起的集簇性DNA损伤会造成细胞突变、 癌变和凋亡。 促进肿瘤细胞凋亡一直是治愈肿瘤的出发点, 所以集簇性DNA损伤已经成为放射生物学领域研究的热点问题。 由于其提取和检测方法多样, 但并没有一个详细和完整的方案对集簇性DNA损伤进行透彻分析。 综述了集簇性DNA损伤的特点和详细讨论了集簇性DNA损伤最新研究进展, 简介了集簇性DNA损伤的研究方法, 以期为集簇性DNA损伤在放疗中的研究提供一些参考。 Clustered DNA damage which caused by high LET heavy ion radiation can lead to mutation, tumorigenesis and apoptosis. Promoting apoptosis of cancer cells is always the basis of cancer treatment. Clustered DNA damage has been the hot topic in radiobiology. The detect method is diversity, but there is not a detail and complete protocol to analyze clustered DNA damage. In order to provide reference for clustered DNA damage in the radiotherapy study, the clustered DNA damage characteristics, the latest progresses on clustered DNA damage and the detecting methods are reviewed and discussed in deteil in this paper.     

离子辐照单晶Si损伤效应的研究

回顾了低能离子注入单晶Si经由核弹性碰撞引起的损伤特征及其常规的研究方法,介绍了快重离子辐照单晶Si经由电子能损引起的损伤特点及研究现状,并对该领域的研究作了展望. The radiation damage in silicon induced by low energy ion implantation was briefly reviewed together with a short introduction to the common techniques in the area. The damage characteristics of swift heavy ion irradiation in silicon and its investigations were introduced with emphasis on the effects induced by processes of electronic energy losses. It is shown that swift heavy ion can induce defects far beyond the projected range and up to 28 MeV/μm the electronic energy ...     

硅微条探测器的辐射损伤试验

测量了硅微条探测器在辐照前后的坪曲线、脉冲高度与偏置电压的关系，及辐照后的总漏电流和黑洞的大小.     

重离子辐射权重因数与辐射损伤模型研究进展

以第五届国际重离子在生物医学中应用会议和第十届国际辐射研究大会为背景,讨论了重离子生物学效应因数、辐射损伤生物物理模型和物理参数的表征等问题． Based on the fifth workshop on heavy charged particles in biology and medicine and the 10 th international congress of radiation research,the biological effects of heavy ions and biophysical models of heavy ions are discussed.     

钨酸铅晶体的辐照损伤研究

报道对钨酸铅晶体作低剂量辐照损伤研究的实验装置、方法、和结果.利用北京计量科学研究院的小型⁶⁰Co放射源对4块钨酸铅晶体作了辐照损伤的实验,发现光产额随辐照剂量的增加呈现指数衰减,最后趋于饱和.     

辐射致DNA损伤及相关生物-化学-物理问题(英文)

介绍了在DNA辐射损伤以及相关生物、物理、化学问题的一些研究工作。重点是径迹结构、DNA双链断裂和细胞学终点的关系。P53-Mdm2负反馈回路在DNA损伤的细胞响应方面起重要作用,用一个简单的模型研究了P53-Mdm2负反馈回路相互作用的动力学行为。Some of recent works are presented on radiation induced DNA damage being carried out at China Institute of Atomic Energy （CIAE） and related bio-chemi-physical problems. Emphasis is placed on track structure and its relation to the cell end-point, and a simple model proposed to study the dynamical behavior of P53-Mdm2 interaction which plays pivotal role in cellular response to DNA damage.     

Serial Femtosecond Crystallography

X-ray free-electron lasers produce brief flashes of X-rays that are of about a billion times higher peak brightness than achievable from storage ring sources. Such a tremendous jump in X-ray source capabilities, which came in 2009 when the Linac Coherent Light Source began operations, was unprecedented in the history of X-ray science. Protein structure determination through the method of macromolecular crystallography has consistently benefited from the many increases in source performance from rotating anodes to all generations of synchrotron facilities. But when confronted with the prospects of such bright beams for structural biology, enthusiastic proposals were tempered by trepidation of the effects of such beams on samples and challenges to record data [1 M. Wilmanns, J. Synchr. Rad. 7, 41 (2000).[Crossref], [PubMed] , [Google Scholar]]. A decade after these discussions (and others in the USA) on the applications of X-ray FELs for biology, the first experiments took place at LCLS, giving results that fulfilled many of the dreams of the early visionaries. In particular, the concept that diffraction representing the pristine object could be recorded before the X-ray pulse completely vaporizes the object was validated [2 H.N. Chapman, Nature 470, 73 (2011).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]], confirming predictions [3 R. Neutze, Nature 406, 753 (2000).[Crossref], [Web of Science ®] , [Google Scholar]] that established dose limits could be vastly exceeded using femtosecond-duration pulses. The first experiments illuminated a path to achieve room-temperature structures free of radiation damage, from samples too small to provide useful data at synchrotron facilities, as well as providing the means to carry out time-resolved crystallography at femtoseconds to milliseconds. In the five years since, progress has been substantial and rapid, invigorating the field of macromolecular crystallography [4 J.C.H. Spence and H.N. Chapman, Phi. Trans. Roy. Soc. B 369, 20130309 (2014).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar], 5 I. Schlichting, IUCrJ 2, 246 (2015).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]. This phase of development is far from over, but with both the LCLS and the SPring-8 Ångström Compact Free-electron Laser (SACLA) providing facilities for measurements, the benefits of X-ray FELs are already being translated into new biological insights.     

Damage Mechanism Analysis and Protection Method of Ionizing Radiation Based on Electromagnetic Radiation Characteristics

Russian Physics Journal - This paper studies the damage mechanism and protection method of ionizing radiation damage based on electromagnetic radiation characteristics. In this paper, the...     

不锈钢辐射损伤随温度和剂量的变化(英文)

用重离子辐照模拟和正电子湮没寿命技术研究了改进型316L不锈钢在21 和33 dpa辐照剂量下的辐照损伤在室温到802 °C温度范围随辐照温度变化和室温下0—100 dpa剂量范围随辐照剂量变化. 在580 °C左右实验观察到辐照肿胀峰， 在21 和33 dpa辐照剂量下相应的空位团分别由14和19个空位组成， 尺度分别为0.68 和0.82 nm. 空位团尺寸随辐照剂量增加， 在100 dpa时空位团由8个空位组成， 尺度为0.55 nm. 实验结果表明， 在改进型316L不锈钢中辐照损伤随辐照温度变化更灵敏.     

水溶液中DNA紫外辐射损伤的分子机制研究

以激光喇曼光谱分析技术,对不同紫外辐射时间条件下ＤＮＡ在水溶液中产生的损伤状况进行研究,结果表明,体外条件下单纯ＤＮＡ水溶液中由紫外辐射直接造成Ｃ→Ｔ的可能性（具体反映在Ｃ→Ｕ这一过程中）是不存在的。胞嘧啶有Ｃ４原子处氨基减少可能,但并无假设衍生形成的尿嘧啶的Ｃ４Ｏ增色表现,不支持胞嘧啶脱氨基直接转变为酮式（成为尿嘧啶）的模型。胞嘧喧Ｎ４Ｈ变形振动的减色似可能证明胞嘧啶的亚氨基化,６１６ｃｍ＾－１     

Damage of Dusty Optical Elements in the Field of Continuous-Wave Laser Radiation

The structure and properties of high-pressure phases of iron nitrides Fe₇N₃ in the pressure range of 50–150 GPa have been studied with ab initio calculations within the electron density functional theory. A new phase Amm2-Fe₇N₃, which is the most energetically favorable in the pressure range of 43–128 GPa, has been found using the USPEX (Universal Structure Predictor: Evolutionary Xtallography) algorithms. It has been thermodynamically shown that another high-pressure phase β-Fe₇N₃ is isostructural to a similar phase of iron carbide. The elastic properties have been calculated for all modifications ε-, β-, and Amm2-Fe₇N₃ stable at high pressures.     

Synergistic Effect of Triple Ion Beams on Radiation Damage in CLAM Steel

The synergistic effect of triple ion beams is investigated by simultaneous and scquential irradiations of gold, hydrogen and helium ions on the low activation martensitie steel （CLAM） developed in China. The depth profile measurements of the positron annihilation Doppler broadening S parameter are carried out as a function of slow- positron beam energy to examine the produced radiation damage. The synergistic effect of displacement damage and hydrogen and helium on the formation of radiation damage is clearly observed. In the preset case ,this effect suppresses the radiation damage in the CLAM steel due to the helium and/or hydrogen filling of vacancy clusters.