Ted Janssen, Gervais Chapuis, and Marc de Boissieu
- Published in print:
- 2007
- Published Online:
- September 2007
- ISBN:
- 9780198567776
- eISBN:
- 9780191718335
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198567776.001.0001
- Subject:
- Physics, Crystallography
Until the 1970s, all materials studied consisted of periodic arrays of unit cells, or were amorphous. In the last decades a new class of solid state matter, called aperiodic crystals, has been found. ...
More
Until the 1970s, all materials studied consisted of periodic arrays of unit cells, or were amorphous. In the last decades a new class of solid state matter, called aperiodic crystals, has been found. It is a long range ordered structure, but without lattice periodicity. It is found in a wide range of materials: organic and anorganic compounds, minerals (including a substantial portion of the earths crust), and metallic alloys, under various pressures and temperatures. Because of the lack of periodicity, the usual techniques for the study of structure and physical properties no longer work, and new techniques have to be developed. This book deals with the characterization of the structure, the structure determination, and the study of the physical properties, especially dynamical and electronic properties of aperiodic crystals. The treatment is based on a description in a space with more dimensions than three, the so-called superspace. This allows us to generalise the standard crystallography and to look differently at the dynamics. The three main classes of aperiodic crystals, modulated phases, incommensurate composites, and quasicrystals are treated from a unified point of view, which stresses the similarities of the various systems.Less
Until the 1970s, all materials studied consisted of periodic arrays of unit cells, or were amorphous. In the last decades a new class of solid state matter, called aperiodic crystals, has been found. It is a long range ordered structure, but without lattice periodicity. It is found in a wide range of materials: organic and anorganic compounds, minerals (including a substantial portion of the earths crust), and metallic alloys, under various pressures and temperatures. Because of the lack of periodicity, the usual techniques for the study of structure and physical properties no longer work, and new techniques have to be developed. This book deals with the characterization of the structure, the structure determination, and the study of the physical properties, especially dynamical and electronic properties of aperiodic crystals. The treatment is based on a description in a space with more dimensions than three, the so-called superspace. This allows us to generalise the standard crystallography and to look differently at the dynamics. The three main classes of aperiodic crystals, modulated phases, incommensurate composites, and quasicrystals are treated from a unified point of view, which stresses the similarities of the various systems.
Dennis Sherwood and Jon Cooper
- Published in print:
- 2010
- Published Online:
- January 2011
- ISBN:
- 9780199559046
- eISBN:
- 9780191595028
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199559046.001.0001
- Subject:
- Physics, Crystallography
This book presents a complete account of the theory of the diffraction of X-rays by crystals with particular reference to the processes of determining the structures of protein molecules. The book ...
More
This book presents a complete account of the theory of the diffraction of X-rays by crystals with particular reference to the processes of determining the structures of protein molecules. The book develops from first principles all relevant mathematics, diffraction, and wave theory. The practical aspects of sample preparation and X-ray data collection using both laboratory and synchrotron sources are covered along with data analysis at both the theoretical and practical levels. The important role played by the Patterson function in structure analysis by both molecular replacement and experimental phasing approaches is covered, as are methods for improving the resulting electron density map. The theoretical basis of methods used in refinement of protein crystal structures are then covered in depth along with the crucial task of defining the binding sites of ligands and drug molecules. The complementary roles of other diffraction methods which reveal further detail of great functional importance in a crystal structure are outlined.Less
This book presents a complete account of the theory of the diffraction of X-rays by crystals with particular reference to the processes of determining the structures of protein molecules. The book develops from first principles all relevant mathematics, diffraction, and wave theory. The practical aspects of sample preparation and X-ray data collection using both laboratory and synchrotron sources are covered along with data analysis at both the theoretical and practical levels. The important role played by the Patterson function in structure analysis by both molecular replacement and experimental phasing approaches is covered, as are methods for improving the resulting electron density map. The theoretical basis of methods used in refinement of protein crystal structures are then covered in depth along with the crucial task of defining the binding sites of ligands and drug molecules. The complementary roles of other diffraction methods which reveal further detail of great functional importance in a crystal structure are outlined.
William Clegg, Alexander J Blake, Jacqueline M Cole, John S O Evans, Peter Main, Simon Parsons, and David J Watkin (eds)
- Published in print:
- 2009
- Published Online:
- September 2009
- ISBN:
- 9780199219469
- eISBN:
- 9780191722516
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199219469.001.0001
- Subject:
- Physics, Crystallography
This book presents a less mathematical approach to X-ray crystal structure determination than is given in some detailed texts and concentrates on practical aspects. The book provides the necessary ...
More
This book presents a less mathematical approach to X-ray crystal structure determination than is given in some detailed texts and concentrates on practical aspects. The book provides the necessary conceptual framework for understanding and applying the techniques described, but also gives practical advice on topics such as growing crystals, solving and refining structures, and understanding and using the results. There are also plenty of worked examples and problems provided (with answers), to reinforce the material presented. The book is based on the intensive course run by the Chemical Crystallography Group of the British Crystallographic Association every two years, and the material is drawn from the 2007 and 2009 courses. Much of the material of the first edition in 2001 has been significantly updated and expanded, and some new topics have been added. The approach to several of the topics is somewhat different as a result of changes in the authorship and the course teaching team. These changes reflect developments in the subject.Less
This book presents a less mathematical approach to X-ray crystal structure determination than is given in some detailed texts and concentrates on practical aspects. The book provides the necessary conceptual framework for understanding and applying the techniques described, but also gives practical advice on topics such as growing crystals, solving and refining structures, and understanding and using the results. There are also plenty of worked examples and problems provided (with answers), to reinforce the material presented. The book is based on the intensive course run by the Chemical Crystallography Group of the British Crystallographic Association every two years, and the material is drawn from the 2007 and 2009 courses. Much of the material of the first edition in 2001 has been significantly updated and expanded, and some new topics have been added. The approach to several of the topics is somewhat different as a result of changes in the authorship and the course teaching team. These changes reflect developments in the subject.
GAUTAM R. DESIRAJU and THOMAS STEINER
- Published in print:
- 2001
- Published Online:
- January 2010
- ISBN:
- 9780198509707
- eISBN:
- 9780191708206
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198509707.003.0006
- Subject:
- Physics, Crystallography
The weak hydrogen bond was first identified in 1935, but it was only in the early 1990s that it really permeated into the consciousness of chemists and biologists. It only seems natural that this ...
More
The weak hydrogen bond was first identified in 1935, but it was only in the early 1990s that it really permeated into the consciousness of chemists and biologists. It only seems natural that this interaction was explored first using spectroscopy, followed by crystallography. In structural supramolecular chemistry, a crystal structure is often not the result of hierarchic interaction preferences but a convolution of a large number of strong and weak interactions, each of which affect the rest intimately. Methods for codification of crystal structures must take this into account if they are to be accurate and useful. Of course, the goal of a subject like crystal engineering is to design systems where the interaction preferences are hierarchic, or in other words where the interaction interference is at a minimum. However, most crystal structures are not so predictable and the challenge posed by weak hydrogen bonding effects to the dogma of crystal engineering remains a real one.Less
The weak hydrogen bond was first identified in 1935, but it was only in the early 1990s that it really permeated into the consciousness of chemists and biologists. It only seems natural that this interaction was explored first using spectroscopy, followed by crystallography. In structural supramolecular chemistry, a crystal structure is often not the result of hierarchic interaction preferences but a convolution of a large number of strong and weak interactions, each of which affect the rest intimately. Methods for codification of crystal structures must take this into account if they are to be accurate and useful. Of course, the goal of a subject like crystal engineering is to design systems where the interaction preferences are hierarchic, or in other words where the interaction interference is at a minimum. However, most crystal structures are not so predictable and the challenge posed by weak hydrogen bonding effects to the dogma of crystal engineering remains a real one.
Tom Vickers
- Published in print:
- 2005
- Published Online:
- January 2008
- ISBN:
- 9780198565932
- eISBN:
- 9780191714016
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198565932.003.0013
- Subject:
- Mathematics, History of Mathematics
This chapter discusses applications of the Pilot ACE. These applications include linear equations, photogrammetry, traffic simulation, matrix programmes, demonstration programmes, and ...
More
This chapter discusses applications of the Pilot ACE. These applications include linear equations, photogrammetry, traffic simulation, matrix programmes, demonstration programmes, and crystallography. The Pilot ACE was a highly successful computer, earning around £100,000 in its four years of life.Less
This chapter discusses applications of the Pilot ACE. These applications include linear equations, photogrammetry, traffic simulation, matrix programmes, demonstration programmes, and crystallography. The Pilot ACE was a highly successful computer, earning around £100,000 in its four years of life.
Georgina Ferry
- Published in print:
- 2011
- Published Online:
- January 2013
- ISBN:
- 9780197264812
- eISBN:
- 9780191754029
- Item type:
- chapter
- Publisher:
- British Academy
- DOI:
- 10.5871/bacad/9780197264812.003.0006
- Subject:
- Sociology, Migration Studies (including Refugee Studies)
This chapter focuses on Austrian-born molecular biologist Max Perutz (1914–2002). Perutz was one of twenty scientific refugees from continental Europe who went on to win Nobel Prizes. A chemist and ...
More
This chapter focuses on Austrian-born molecular biologist Max Perutz (1914–2002). Perutz was one of twenty scientific refugees from continental Europe who went on to win Nobel Prizes. A chemist and molecular biologist, he led the first successful attempt to discover the three-dimensional structure of protein molecules using X-ray crystallography, for which he shared the 1962 Nobel Prize. He was the founding chairman of the Laboratory of Molecular Biology in Cambridge, an institution that continues to thrive and counts thirteen Nobel Prize-winners among those who have spent time in its laboratories. Although Perutz applied to the Society for the Protection of Science and Learning (SPSL) for funding, in the event he did not need their money. His case, however, offers an excellent example of the emotional and practical support SPSL's officers extended to all academics who found themselves in precarious situations in the years following the rise to power of the Nazis in Germany and their subsequent conquest or annexation of neighbouring countries.Less
This chapter focuses on Austrian-born molecular biologist Max Perutz (1914–2002). Perutz was one of twenty scientific refugees from continental Europe who went on to win Nobel Prizes. A chemist and molecular biologist, he led the first successful attempt to discover the three-dimensional structure of protein molecules using X-ray crystallography, for which he shared the 1962 Nobel Prize. He was the founding chairman of the Laboratory of Molecular Biology in Cambridge, an institution that continues to thrive and counts thirteen Nobel Prize-winners among those who have spent time in its laboratories. Although Perutz applied to the Society for the Protection of Science and Learning (SPSL) for funding, in the event he did not need their money. His case, however, offers an excellent example of the emotional and practical support SPSL's officers extended to all academics who found themselves in precarious situations in the years following the rise to power of the Nazis in Germany and their subsequent conquest or annexation of neighbouring countries.
Mark R. Sanderson
- Published in print:
- 2007
- Published Online:
- September 2007
- ISBN:
- 9780198520979
- eISBN:
- 9780191706295
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198520979.003.0005
- Subject:
- Biology, Biochemistry / Molecular Biology
In the field of macromolecular crystallography, a renaissance occurred in data collection with the advent of two-dimensional area detectors. These rapidly superseded film cameras and diffractometers ...
More
In the field of macromolecular crystallography, a renaissance occurred in data collection with the advent of two-dimensional area detectors. These rapidly superseded film cameras and diffractometers fitted with proportional counters as the tools of choice for macromolecular data collection, resulting in a huge increase in collection speeds. This chapter discusses in-house data collection. Data collection systems consist of four major components: a source of X-rays, focusing mirrors (optics), a motor-driven goniostat and crystal viewing assembly, and an area detector for recording diffracted images. The chapter first describes the components that make up this assembly. Before proceeding to discuss X-ray generators, it defines two terms that are widely used in describing the attributes of X-ray generation: flux and brilliance. Flux is the number of photons per second per mrad, and brilliance is the number of photons per second per unit phase space volume (with units photons/s/mm2/millirad2). These are important values when comparing X-ray generators with different filament and focal spots sizes.Less
In the field of macromolecular crystallography, a renaissance occurred in data collection with the advent of two-dimensional area detectors. These rapidly superseded film cameras and diffractometers fitted with proportional counters as the tools of choice for macromolecular data collection, resulting in a huge increase in collection speeds. This chapter discusses in-house data collection. Data collection systems consist of four major components: a source of X-rays, focusing mirrors (optics), a motor-driven goniostat and crystal viewing assembly, and an area detector for recording diffracted images. The chapter first describes the components that make up this assembly. Before proceeding to discuss X-ray generators, it defines two terms that are widely used in describing the attributes of X-ray generation: flux and brilliance. Flux is the number of photons per second per mrad, and brilliance is the number of photons per second per unit phase space volume (with units photons/s/mm2/millirad2). These are important values when comparing X-ray generators with different filament and focal spots sizes.
Sherin S. Abdel-Meguid
- Published in print:
- 2007
- Published Online:
- September 2007
- ISBN:
- 9780198520979
- eISBN:
- 9780191706295
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198520979.003.0006
- Subject:
- Biology, Biochemistry / Molecular Biology
This chapter begins with a discussion of the theoretical basis of isomorphous replacement. It then discusses the selection of heavy-atom reagents, heavy atoms and their ligands, preparation of ...
More
This chapter begins with a discussion of the theoretical basis of isomorphous replacement. It then discusses the selection of heavy-atom reagents, heavy atoms and their ligands, preparation of heavy-atom derivatives, determination of heavy-atom positions, and refinement of heavy-atom positions.Less
This chapter begins with a discussion of the theoretical basis of isomorphous replacement. It then discusses the selection of heavy-atom reagents, heavy atoms and their ligands, preparation of heavy-atom derivatives, determination of heavy-atom positions, and refinement of heavy-atom positions.
R. J. Morris, A. Perrakis, and V. S. Lamzin
- Published in print:
- 2007
- Published Online:
- September 2007
- ISBN:
- 9780198520979
- eISBN:
- 9780191706295
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198520979.003.0011
- Subject:
- Biology, Biochemistry / Molecular Biology
This chapter casts the high-throughput automation efforts being developed to meet the needs of Structural Genomics initiatives in the framework of an optimization problem. It gives a general overview ...
More
This chapter casts the high-throughput automation efforts being developed to meet the needs of Structural Genomics initiatives in the framework of an optimization problem. It gives a general overview on optimization techniques with a bias specifically towards the problem of crystallographic refinement. This picture is extended as the chapter considers model building, program flow control, decision-making, validation, and automation. Finer details of different approaches are provided in a conclusive review of some popular software packages and pipelines.Less
This chapter casts the high-throughput automation efforts being developed to meet the needs of Structural Genomics initiatives in the framework of an optimization problem. It gives a general overview on optimization techniques with a bias specifically towards the problem of crystallographic refinement. This picture is extended as the chapter considers model building, program flow control, decision-making, validation, and automation. Finer details of different approaches are provided in a conclusive review of some popular software packages and pipelines.
Benoît Masquida, Boris François, Andreas Werner, and Eric Westhof
- Published in print:
- 2007
- Published Online:
- September 2007
- ISBN:
- 9780198520979
- eISBN:
- 9780191706295
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198520979.003.0014
- Subject:
- Biology, Biochemistry / Molecular Biology
The number of RNA crystal structures has increased in an exponential manner mainly due to the fact that RNA is increasingly viewed as a predominant part of biological processes such as translation, ...
More
The number of RNA crystal structures has increased in an exponential manner mainly due to the fact that RNA is increasingly viewed as a predominant part of biological processes such as translation, ribozyme catalysis, and gene regulation, riboswitches, and mRNA-protein interactions, for which the gap in structural knowledge is still deep despite the determination of the crystal structure of the ribosome. Structural studies of the ubiquitous roles of RNA at all levels of cellular processes are starting to be supported by technological developments which enable high-throughput crystallography (HTC). Recently, robotics has entered the field of crystallization. Despite the high cost of these robots, they are highly valuable because they significantly shorten the time to set up experiments as well as multiply the number of possible tests by a 100-fold, just by going to the nanolitre scale in terms of liquid sample handling. They also allow samples to be tested that are too scarce for the usual microlitre-scale techniques. Furthermore, they reduce handling time, which can then be spent on more valuable tasks such as macromolecule purification or structure solving. This chapter presents guidelines to purify and set up RNA oligonucleotides crystallization experiments using a robot. An overview of crystallization robots available on the market will also be given with their advantages and drawbacks.Less
The number of RNA crystal structures has increased in an exponential manner mainly due to the fact that RNA is increasingly viewed as a predominant part of biological processes such as translation, ribozyme catalysis, and gene regulation, riboswitches, and mRNA-protein interactions, for which the gap in structural knowledge is still deep despite the determination of the crystal structure of the ribosome. Structural studies of the ubiquitous roles of RNA at all levels of cellular processes are starting to be supported by technological developments which enable high-throughput crystallography (HTC). Recently, robotics has entered the field of crystallization. Despite the high cost of these robots, they are highly valuable because they significantly shorten the time to set up experiments as well as multiply the number of possible tests by a 100-fold, just by going to the nanolitre scale in terms of liquid sample handling. They also allow samples to be tested that are too scarce for the usual microlitre-scale techniques. Furthermore, they reduce handling time, which can then be spent on more valuable tasks such as macromolecule purification or structure solving. This chapter presents guidelines to purify and set up RNA oligonucleotides crystallization experiments using a robot. An overview of crystallization robots available on the market will also be given with their advantages and drawbacks.
Maninder K. Sohi and Ivan Laponogov
- Published in print:
- 2007
- Published Online:
- September 2007
- ISBN:
- 9780198520979
- eISBN:
- 9780191706295
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198520979.003.0015
- Subject:
- Biology, Biochemistry / Molecular Biology
In the living cell, protein-DNA interactions take place during genetic processes such as chromatin organization, recombination, replication, transcription, and DNA repair. In order to fully ...
More
In the living cell, protein-DNA interactions take place during genetic processes such as chromatin organization, recombination, replication, transcription, and DNA repair. In order to fully understand the mechanism of these processes, study of protein-DNA interactions at atomic level is required. Despite the wealth of knowledge and attempts of several investigators to classify protein-DNA complexes on the basis of structural analysis of well over 200 protein-DNA complexes, the prediction and modelling based on three-dimensional structure or amino acid sequence of a protein and nucleotide sequence of DNA is challenging. X-ray crystallography is the most powerful technique used for structural studies and the development of technology for the production and purification of large quantities of proteins and DNA is vital to its success. Advances in oligonucleotide synthesis have not only provided ease of synthesis of large quantities of pure DNA but also of any required DNA sequence. This has resulted in the crystallization and structure determination of a vast number of DNA oligonucleotides and protein-DNA complexes. Since 1994 there has been a dramatic increase in the number of the protein-DNA complex structures solved annually. The first and most difficult step in the X-ray crystallographic study is the growth of well-diffracting crystals of the protein-DNA complex under investigation. This chapter describes methods employed to purify proteins and DNA for cocrystallization, procedures for crystallization of protein-DNA, and characterization of cocrystals.Less
In the living cell, protein-DNA interactions take place during genetic processes such as chromatin organization, recombination, replication, transcription, and DNA repair. In order to fully understand the mechanism of these processes, study of protein-DNA interactions at atomic level is required. Despite the wealth of knowledge and attempts of several investigators to classify protein-DNA complexes on the basis of structural analysis of well over 200 protein-DNA complexes, the prediction and modelling based on three-dimensional structure or amino acid sequence of a protein and nucleotide sequence of DNA is challenging. X-ray crystallography is the most powerful technique used for structural studies and the development of technology for the production and purification of large quantities of proteins and DNA is vital to its success. Advances in oligonucleotide synthesis have not only provided ease of synthesis of large quantities of pure DNA but also of any required DNA sequence. This has resulted in the crystallization and structure determination of a vast number of DNA oligonucleotides and protein-DNA complexes. Since 1994 there has been a dramatic increase in the number of the protein-DNA complex structures solved annually. The first and most difficult step in the X-ray crystallographic study is the growth of well-diffracting crystals of the protein-DNA complex under investigation. This chapter describes methods employed to purify proteins and DNA for cocrystallization, procedures for crystallization of protein-DNA, and characterization of cocrystals.
Elizabeth E. Fry, Nicola G. A. Abrescia, and David I. Stuart
- Published in print:
- 2007
- Published Online:
- September 2007
- ISBN:
- 9780198520979
- eISBN:
- 9780191706295
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198520979.003.0016
- Subject:
- Biology, Biochemistry / Molecular Biology
This chapter discusses all aspects of the methodology used to solve isometric virus structures with separate case study examples for two demanding examples, the blue tongue virus core (BTV) and ...
More
This chapter discusses all aspects of the methodology used to solve isometric virus structures with separate case study examples for two demanding examples, the blue tongue virus core (BTV) and bacteriophage PRD1, the first structure of an intact virus with an internal membrane.Less
This chapter discusses all aspects of the methodology used to solve isometric virus structures with separate case study examples for two demanding examples, the blue tongue virus core (BTV) and bacteriophage PRD1, the first structure of an intact virus with an internal membrane.
Sherin S. Abdel-Meguid
- Published in print:
- 2007
- Published Online:
- September 2007
- ISBN:
- 9780198520979
- eISBN:
- 9780191706295
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198520979.003.0017
- Subject:
- Biology, Biochemistry / Molecular Biology
This chapter discusses macromolecular crystallography in drug discovery. Currently, all large and most small pharmaceutical and biotechnology companies have invested in macromolecular ...
More
This chapter discusses macromolecular crystallography in drug discovery. Currently, all large and most small pharmaceutical and biotechnology companies have invested in macromolecular crystallography, with protein crystallography now an integral tool of drug discovery. During the last twenty years, the term rational drug design has slowly been replaced with the more precise term structure-based drug design (SBDD).Less
This chapter discusses macromolecular crystallography in drug discovery. Currently, all large and most small pharmaceutical and biotechnology companies have invested in macromolecular crystallography, with protein crystallography now an integral tool of drug discovery. During the last twenty years, the term rational drug design has slowly been replaced with the more precise term structure-based drug design (SBDD).
Jan Sapp
- Published in print:
- 2003
- Published Online:
- September 2007
- ISBN:
- 9780195156195
- eISBN:
- 9780199790340
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195156195.003.0016
- Subject:
- Biology, Evolutionary Biology / Genetics
This chapter focuses on the discovery of DNA. The discovery of DNA as the basis of the gene, how it is reproduced, and how it affects protein synthesis was the pinnacle of life sciences in the 20th ...
More
This chapter focuses on the discovery of DNA. The discovery of DNA as the basis of the gene, how it is reproduced, and how it affects protein synthesis was the pinnacle of life sciences in the 20th century. Gene splicing, recombinant DNA, transgenic organisms (or genetically modified plants and animals), and the patenting of genes from microbes to humans all have roots in fundamental discoveries in molecular biology during the 1950s and 1960s. The molecular approach to the gene involved a merger of microbiology and genetics using three techniques from physics and chemistry: (i) radioisotopes were used to help identify DNA as the basis of the gene; (ii) X-ray crystallography was used to reveal the three-dimensional structure of proteins and of DNA; and (iii) chromatography was used to analyze the composition of DNA and proteins.Less
This chapter focuses on the discovery of DNA. The discovery of DNA as the basis of the gene, how it is reproduced, and how it affects protein synthesis was the pinnacle of life sciences in the 20th century. Gene splicing, recombinant DNA, transgenic organisms (or genetically modified plants and animals), and the patenting of genes from microbes to humans all have roots in fundamental discoveries in molecular biology during the 1950s and 1960s. The molecular approach to the gene involved a merger of microbiology and genetics using three techniques from physics and chemistry: (i) radioisotopes were used to help identify DNA as the basis of the gene; (ii) X-ray crystallography was used to reveal the three-dimensional structure of proteins and of DNA; and (iii) chromatography was used to analyze the composition of DNA and proteins.
William Taussig Scott and Martin X. Moleski
- Published in print:
- 2005
- Published Online:
- July 2005
- ISBN:
- 9780195174335
- eISBN:
- 9780199835706
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/019517433X.001.0001
- Subject:
- Religion, Philosophy of Religion
Michael Polanyi (1891–1976) was born to a Viennese family living in Hungary. After obtaining a medical degree, he served in the Austro-Hungarian army in World War I, then chose Austrian citizenship ...
More
Michael Polanyi (1891–1976) was born to a Viennese family living in Hungary. After obtaining a medical degree, he served in the Austro-Hungarian army in World War I, then chose Austrian citizenship in the aftermath of the war. While on sick leave, he wrote an article on the adsorption of gases that became the foundation for his doctoral research in physical chemistry at Karlsruhe in Germany. In his later work at the Kaiser Wilhelm Institute in Berlin and the University of Manchester in England, Polanyi also worked on crystallography and reaction kinetics. After fleeing to England from Nazi Germany, Polanyi gradually turned away from physical chemistry to studies in economics, social and political analysis, philosophy, theology, and aesthetics. The biography traces the development of Polanyi's theory of tacit, personal knowledge and shows how his scientific career shaped his philosophy of science and his view of religion in general and Christianity and Judaism in particular.Less
Michael Polanyi (1891–1976) was born to a Viennese family living in Hungary. After obtaining a medical degree, he served in the Austro-Hungarian army in World War I, then chose Austrian citizenship in the aftermath of the war. While on sick leave, he wrote an article on the adsorption of gases that became the foundation for his doctoral research in physical chemistry at Karlsruhe in Germany. In his later work at the Kaiser Wilhelm Institute in Berlin and the University of Manchester in England, Polanyi also worked on crystallography and reaction kinetics. After fleeing to England from Nazi Germany, Polanyi gradually turned away from physical chemistry to studies in economics, social and political analysis, philosophy, theology, and aesthetics. The biography traces the development of Polanyi's theory of tacit, personal knowledge and shows how his scientific career shaped his philosophy of science and his view of religion in general and Christianity and Judaism in particular.
William Taussig Scott and Martin X. Moleski
- Published in print:
- 2005
- Published Online:
- July 2005
- ISBN:
- 9780195174335
- eISBN:
- 9780199835706
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/019517433X.003.0004
- Subject:
- Religion, Philosophy of Religion
Fritz Haber hired Polanyi to work in the Fiber Chemistry Group of the Kaiser Wilhelm Institute in Berlin. Polanyi helped develop the rotating-crystal method of X-ray crystallography, made solid ...
More
Fritz Haber hired Polanyi to work in the Fiber Chemistry Group of the Kaiser Wilhelm Institute in Berlin. Polanyi helped develop the rotating-crystal method of X-ray crystallography, made solid contributions to understanding the structure of cellulose, pressed forward with his work on adsorption catalysis and electrostatic dipoles, laid the foundation for transition rate theory in reaction kinetics, and investigated the bond strength of crystals; he was also forced to give up a cherished theory about quantum jumps in reaction kinetics, which taught him an important lesson about how scientists work together to distinguish real discoveries from mistaken surmises. Polanyi married Magda Kemeny on February 21, 1921, in a civil ceremony; their first child, George Michael Polanyi, was born on October 1, 1922.Less
Fritz Haber hired Polanyi to work in the Fiber Chemistry Group of the Kaiser Wilhelm Institute in Berlin. Polanyi helped develop the rotating-crystal method of X-ray crystallography, made solid contributions to understanding the structure of cellulose, pressed forward with his work on adsorption catalysis and electrostatic dipoles, laid the foundation for transition rate theory in reaction kinetics, and investigated the bond strength of crystals; he was also forced to give up a cherished theory about quantum jumps in reaction kinetics, which taught him an important lesson about how scientists work together to distinguish real discoveries from mistaken surmises. Polanyi married Magda Kemeny on February 21, 1921, in a civil ceremony; their first child, George Michael Polanyi, was born on October 1, 1922.
Xiaodong Zou, Sven Hovmöller, and Peter Oleynikov
- Published in print:
- 2011
- Published Online:
- January 2012
- ISBN:
- 9780199580200
- eISBN:
- 9780191731211
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199580200.003.0001
- Subject:
- Physics, Crystallography
The historical introduction covers the parallel developments in EM on inorganic and biological samples. Vainshtein, Pinsker and Zvyagin in Moscow solved structures from electron-diffraction patterns ...
More
The historical introduction covers the parallel developments in EM on inorganic and biological samples. Vainshtein, Pinsker and Zvyagin in Moscow solved structures from electron-diffraction patterns in the 1950s. Aaron Klug in 1968 pioneered computer image processing of EM images and realised that the crystallographic structure factor phase information can be read out directly in numbers from the Fourier transform. A few years later the EM optics was powerful enough to allow metals to be seen in oxides. The first determination of atomic coordinates in a crystal from EM images was done in 1984. Compared to X-ray crystallography, electron microscopy has some advantages; crystals a million times smaller (even defects) can be studied and the crystallographic structure factor phases can be read out numerically. Drawbacks are radiation damage (especially for organics) and multiple diffraction.Less
The historical introduction covers the parallel developments in EM on inorganic and biological samples. Vainshtein, Pinsker and Zvyagin in Moscow solved structures from electron-diffraction patterns in the 1950s. Aaron Klug in 1968 pioneered computer image processing of EM images and realised that the crystallographic structure factor phase information can be read out directly in numbers from the Fourier transform. A few years later the EM optics was powerful enough to allow metals to be seen in oxides. The first determination of atomic coordinates in a crystal from EM images was done in 1984. Compared to X-ray crystallography, electron microscopy has some advantages; crystals a million times smaller (even defects) can be studied and the crystallographic structure factor phases can be read out numerically. Drawbacks are radiation damage (especially for organics) and multiple diffraction.
Joachim Frank
- Published in print:
- 2006
- Published Online:
- April 2010
- ISBN:
- 9780195182187
- eISBN:
- 9780199893416
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195182187.003.0001
- Subject:
- Biology, Biochemistry / Molecular Biology
This introductory chapter begins with an appreciation of the unique position of electron microscopy in biological research as it bridges a wide gap between X-ray crystallography and light microscopy. ...
More
This introductory chapter begins with an appreciation of the unique position of electron microscopy in biological research as it bridges a wide gap between X-ray crystallography and light microscopy. The scope of this book is defined to cover three-dimensional imaging of molecular assemblies that exist in an in vitro sample in large numbers with identical or near-identical structure. Only with such samples it is possible to collect large numbers of projection images suitable for averaging and three-dimensional reconstruction. The fact that molecules can be imaged as single, isolated particles embedded in ice (“crystallography without crystals”) makes the techniques described in this book uniquely suited to image molecular machines in their various processing states. In sharp contrast, electron tomography, not covered in this book, is concerned with the three-dimensional imaging of “unique” objects that may be an organelle or slice of a cell. The vision of a unified structural analysis of macromolecules is articulated, which would lead to an integration of results from cryo-EM, X-ray crystallography and NMR, and a cross-fertilization among these disciplines. The chapter concludes by making the point that the development of single-particle reconstruction would not have been possible without the vast increase in computer power seen in the past decades.Less
This introductory chapter begins with an appreciation of the unique position of electron microscopy in biological research as it bridges a wide gap between X-ray crystallography and light microscopy. The scope of this book is defined to cover three-dimensional imaging of molecular assemblies that exist in an in vitro sample in large numbers with identical or near-identical structure. Only with such samples it is possible to collect large numbers of projection images suitable for averaging and three-dimensional reconstruction. The fact that molecules can be imaged as single, isolated particles embedded in ice (“crystallography without crystals”) makes the techniques described in this book uniquely suited to image molecular machines in their various processing states. In sharp contrast, electron tomography, not covered in this book, is concerned with the three-dimensional imaging of “unique” objects that may be an organelle or slice of a cell. The vision of a unified structural analysis of macromolecules is articulated, which would lead to an integration of results from cryo-EM, X-ray crystallography and NMR, and a cross-fertilization among these disciplines. The chapter concludes by making the point that the development of single-particle reconstruction would not have been possible without the vast increase in computer power seen in the past decades.
John Jenkin
- Published in print:
- 2007
- Published Online:
- January 2008
- ISBN:
- 9780199235209
- eISBN:
- 9780191715631
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199235209.001.0001
- Subject:
- Physics, History of Physics
This book describes how Lawrence and William Bragg, son and father, invented, developed, and led the scientific field of X-ray crystallography for fifty years, transforming much of modern science. ...
More
This book describes how Lawrence and William Bragg, son and father, invented, developed, and led the scientific field of X-ray crystallography for fifty years, transforming much of modern science. Attention is also given to William's early belief in the dual wave-particle nature of radiation, his eventual vindication, and the crucial roles both played during The Great War. The book highlights the intimate relationship between father and son that made their project possible, and emphasizes wider family and human relationships. For the first time, close attention is given to the crucial twenty-three-year period in Australia (1886-1909) — when William matured into a notable scientist and Lawrence was born, raised, and educated — thereby providing a new vision of the colonial science experience. Finally, the following published criticisms of Lawrence Bragg are shown to be false: that his work had no great influence on physics then or later; that as a classical physicist in the age of quantum theory he was a scientific dinosaur; that he was ignorant of chemistry and biology and disinterested in both; that his relationship with his father was tense and cool, and with his mother distant.Less
This book describes how Lawrence and William Bragg, son and father, invented, developed, and led the scientific field of X-ray crystallography for fifty years, transforming much of modern science. Attention is also given to William's early belief in the dual wave-particle nature of radiation, his eventual vindication, and the crucial roles both played during The Great War. The book highlights the intimate relationship between father and son that made their project possible, and emphasizes wider family and human relationships. For the first time, close attention is given to the crucial twenty-three-year period in Australia (1886-1909) — when William matured into a notable scientist and Lawrence was born, raised, and educated — thereby providing a new vision of the colonial science experience. Finally, the following published criticisms of Lawrence Bragg are shown to be false: that his work had no great influence on physics then or later; that as a classical physicist in the age of quantum theory he was a scientific dinosaur; that he was ignorant of chemistry and biology and disinterested in both; that his relationship with his father was tense and cool, and with his mother distant.
Giovanni Ferraris, Emil Makovicky, and Stefano Merlino
- Published in print:
- 2008
- Published Online:
- September 2008
- ISBN:
- 9780199545698
- eISBN:
- 9780191712111
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199545698.001.0001
- Subject:
- Physics, Crystallography
This book provides a treatment of theories and applications in the rapidly expanding field of the crystallography of modular materials. Molecules are the natural modules from which molecular ...
More
This book provides a treatment of theories and applications in the rapidly expanding field of the crystallography of modular materials. Molecules are the natural modules from which molecular crystalline structures are built. In recent years, the attention has been focused on complex modules as the basis for a systematic description of polytypes and homologous/polysomatic series (modular structures). This representation is applied to the modelling of unknown structures and understanding nanoscale defects and intergrowths in materials. The Order/Disorder (OD) theory is fundamental to developing a systematic theory of polytypism, dealing with those structures based on both ordered and disordered stacking of one or more layers. Twinning at both unit cell and microscale, together with disorder, causes many problems to the determination of crystal structures. The book develops the theory of twinning with the inclusion of worked examples. In spite of the increasing use of the concepts of modular crystallography for characterizing, understanding, and tailoring technological crystalline materials, this book offers a unified treatment of the results, which are spread across many different journal and papers published over the last twenty years.Less
This book provides a treatment of theories and applications in the rapidly expanding field of the crystallography of modular materials. Molecules are the natural modules from which molecular crystalline structures are built. In recent years, the attention has been focused on complex modules as the basis for a systematic description of polytypes and homologous/polysomatic series (modular structures). This representation is applied to the modelling of unknown structures and understanding nanoscale defects and intergrowths in materials. The Order/Disorder (OD) theory is fundamental to developing a systematic theory of polytypism, dealing with those structures based on both ordered and disordered stacking of one or more layers. Twinning at both unit cell and microscale, together with disorder, causes many problems to the determination of crystal structures. The book develops the theory of twinning with the inclusion of worked examples. In spite of the increasing use of the concepts of modular crystallography for characterizing, understanding, and tailoring technological crystalline materials, this book offers a unified treatment of the results, which are spread across many different journal and papers published over the last twenty years.
