The Experts below are selected from a list of 228 Experts worldwide ranked by ideXlab platform
Alexander Mcpherson - One of the best experts on this subject based on the ideXlab platform.
-
Macromolecular Crystal growth investigations using atomic force microscopy
Journal of Synchrotron Radiation, 2003Co-Authors: Alexander Mcpherson, Yurii G. Kuznetsov, A. J. Malkin, M. PlompAbstract:Direct visualization of Macromolecular Crystal growth using atomic force microscopy (AFM) has provided a powerful tool in the delineation of mechanisms and the kinetics of the growth process. It has further allowed us to evaluate the wide variety of impurities that are incorporated into Crystals of proteins, nucleic acids, and viruses. It is possible, using AFM, to image the defects and imperfections that afflict these Crystals, the impurity layers that poison their surfaces, and the consequences of various factors on morphological development. All of these can be recorded under normal growth conditions, in native mother liquors, over time intervals ranging from minutes to days, and at the molecular level.
-
Biopolymers Online - Crystallization of Proteins, Nucleic Acids, and Viruses for X‐ray Diffraction Analysis
Biopolymers Online, 2003Co-Authors: Alexander Mcpherson, Robert Cudney, Sam PatelAbstract:Introduction Solubility and Supersaturation Properties of Macromolecular Crystals Preparation of Samples Precipitants and Their Effects The Use of Temperature for Crystallization Creating Supersaturation – Methodology Factors Affecting Crystallization Screening and Optimization Theoretical Contributions to Macromolecular Crystal Growth Future Trends
-
Macromolecular Crystal growth as revealed by atomic force microscopy
Journal of structural biology, 2003Co-Authors: Alexander Mcpherson, Yu G Kuznetsov, A. J. Malkin, M. PlompAbstract:Direct visualization of Macromolecular Crystal growth using atomic force microscopy (AFM) has provided a powerful tool in the delineation of mechanisms and the kinetics of the growth process. It has further allowed us to evaluate the wide variety of impurities that are incorporated into Crystals of proteins, nucleic acids, and viruses. We can, using AFM, image the defects and imperfections that afflict these Crystals, the impurity layers that poison their surfaces, and the consequences of various factors on morphological development. All of these can be recorded under normal growth conditions, in native mother liquors, over time intervals ranging from minutes to days, and at the molecular level.
-
the influence of precipitant concentration on Macromolecular Crystal growth mechanisms
Journal of Crystal Growth, 2001Co-Authors: Yu G Kuznetsov, A. J. Malkin, Alexander McphersonAbstract:Abstract Atomic force microscopy was applied to investigate the influence of protein and precipitant (sodium-potassium tartrate) concentration on thaumatin Crystal growth mechanisms. At constant protein concentration, a decrease of salt concentration from 0.8 to 0.085 M caused a transition of the Crystal growth mechanism from two-dimensional nucleation to dislocation growth. At different, fixed concentrations of salt, the protein concentration, which does not induce multiple Crystal nucleation, was increased from 8 to 60 mg/ml with corresponding increases in the tangential velocity of growth steps from 5 to 17.5 nm/s. Results from these experiments suggest that a highly concentrated protein solution, as might be found in a protein rich phase, may not induce Crystal nucleation, but can promote Crystal growth if screw dislocations are present in the Crystal.
-
Atomic force microscopy in the study of Macromolecular Crystal growth.
Annual review of biophysics and biomolecular structure, 2000Co-Authors: Alexander Mcpherson, Alexander J Malkin, Kuznetsov YugAbstract:▪ Abstract Atomic force microscopy (AFM) has been used to study protein, nucleic acid, and virus Crystals in situ, in their mother liquors, as they grow. From sequential AFM images taken at brief intervals over many hours, or even days, the mechanisms and kinetics of the growth process can be defined. The appearance of both two- and three-dimensional nuclei on Crystal surfaces have been visualized, defect structures of Crystals were clearly evident, and defect densities of Crystals were also determined. The incorporation of a wide range of impurities, ranging in size from molecules to microns or larger microCrystals, and even foreign particles were visually recorded. From these observations and measurements, a more complex understanding of the detailed character of Macromolecular Crystals is emerging, one that reveals levels of complexity previously unsuspected. The unique features of these Crystals, apparently in AFM images, undoubtedly influence the diffraction properties of the Crystals and the quality...
G J Bunick - One of the best experts on this subject based on the ideXlab platform.
-
Annealing Macromolecular Crystals.
Methods in molecular biology (Clifton N.J.), 2007Co-Authors: B. Leif Hanson, G J BunickAbstract:The process of Crystal annealing has been used to improve the quality of diffraction from Crystals that would otherwise be discarded for displaying unsatisfactory diffraction after flash cooling. Although techniques and protocols vary, Macromolecular Crystals are annealed by warming the flash-cooled Crystal, then flash cooling it again. To apply Macromolecular Crystal annealing, a flash-cooled Crystal displaying unacceptably high mosaicity or diffraction from ice is removed from the goniometer and immediately placed in cryoprotectant buffer. The Crystal is incubated in the buffer at either room temperature or the temperature at which the Crystal was grown. After about 3 min, the Crystal is remounted in the loop and flash cooled. In situ annealing techniques, where the cold stream is diverted and the Crystal allowed to warm on the loop prior to flash cooling, are variations of annealing that appears to work best when large solvent channels are not present in the Crystal lattice or the solvent content of the Crystal is relatively low.
-
The well-tempered protein Crystal: annealing Macromolecular Crystals.
Methods in enzymology, 2003Co-Authors: B. Leif Hanson, J M Harp, G J BunickAbstract:Publisher Summary This chapter discusses about the annealing Macromolecular Crystals. Annealing techniques can overcome increased Crystal mosaicity after flash cooling. These techniques, involving the heating and cooling of a Crystal, can be referred to as annealing or tempering the Macromolecular Crystal. The term annealing implies a slow or gradual cooling of material after heating. There are several annealing techniques in use today. Macromolecular Crystal annealing (MCA) refers to the specific protocol that introduced the concept of annealing and that has been developed originally with Crystals of chromatin structural elements (nucleosome core particle). The Crystal is incubated in the buffer at either room temperature or the temperature at which the Crystal is grown. The single most important precondition for MCA is that the Crystal must be stable in the cryoprotectant during the period of incubation before the second flash cooling. The chapter presents the list of macromolecules for which annealing has been reported. Finally, this chapter elucidates the mode of action of annealing by explaining the results from the annealing experiments in terms of the mosaic-block model of the Crystals.
-
New techniques in Macromolecular cryoCrystallography: Macromolecular Crystal annealing and cryogenic helium.
Journal of structural biology, 2003Co-Authors: B. Leif Hanson, Constance A. Schall, G J BunickAbstract:CryoCrystallography is used today for almost all X-ray diffraction data collection at synchrotron beam lines, with rotating-anode generators, and micro X-ray sources. Despite the widespread use of flash-cooling to place Macromolecular Crystals in the cryogenic state, its use can ruin Crystals, trips to the synchrotron, and sometimes even an entire project. Annealing of Macromolecular Crystals takes little time, requires no specialized equipment, and can save Crystallographic projects that might otherwise end in failure. Annealing should be tried whenever initial flash-cooling causes an unacceptable increase in mosaicity, results in ice rings, fails to provide adequate diffraction quality, or causes a Crystal to be positioned awkwardly. Overall, annealing improves the quality of data and overall success rate at synchrotron beam lines. Its use should be considered whenever problems arise with a flash-cooled Crystal. Helium is a more efficient cryogen than nitrogen and will deliver lower temperatures. Experiments suggest that when Crystals are cooled with He rather than N2, Crystals maintain order and high-resolution data are less affected by increased radiation load. Individually or in combination, these two techniques can enhance the success of Crystallographic data collection, and their use should be considered essential for high-throughput programs.
-
Macromolecular Crystal annealing: evaluation of techniques and variables.
Acta crystallographica. Section D Biological crystallography, 1999Co-Authors: J M Harp, B L Hanson, D E Timm, G J BunickAbstract:Additional examples of successful application of Macromolecular Crystal annealing are presented. A qualitative evaluation of variables related to the annealing process was conducted using a variety of Macromolecular Crystals to determine in which cases parameters may be varied and in which cases the original Macromolecular Crystal annealing protocol is preferred. A hypothesis is presented relating the solvent content of the Crystal to the specific protocol necessary for the successful application of annealing.
-
Macromolecular Crystal annealing: overcoming increased mosaicity associated with cryoCrystallography.
Acta Crystallographica Section D Biological Crystallography, 1998Co-Authors: J M Harp, D E Timm, G J BunickAbstract:Although cryogenic data collection has become the method of choice for Macromolecular Crystallography, the flash-cooling step can dramatically increase the mosaicity of some Crystals. Macromolecular Crystal annealing significantly reduces the mosaicity of flash-cooled Crystals without affecting molecular structure. The process, which cycles a flash-cooled Crystal to ambient temperature and back to cryogenic temperature, is simple, quick and requires no special equipment. The annealing process has been applied to Crystals of several different macromolecules grown from different precipitants and using a variety of cryoprotectants. The protocol for Macromolecular Crystal annealing also has been applied to restore diffraction from flash-cooled Crystals that were mishandled during transfer to or from cryogenic storage. These results will be discussed in relation to Crystal mosaicity and effects of radiation damage in flash-cooled Crystals.
Gloria E. O. Borgstahl - One of the best experts on this subject based on the ideXlab platform.
-
Characterizing pathological imperfections in Macromolecular Crystals: lattice disorders and modulations.
Crystallography reviews, 2019Co-Authors: Jeffrey J. Lovelace, Gloria E. O. BorgstahlAbstract:Macromolecular Crystal structure determination can be complicated or brought to a halt by Crystal imperfections. These issues motivated us to write up what we affectionately call ‘The Definitive Hi...
-
How to assign a (3 + 1)-dimensional superspace group to an incommensurately modulated biological Macromolecular Crystal
Journal of Applied Crystallography, 2017Co-Authors: Jason Porta, Jeffrey J. Lovelace, Gloria E. O. BorgstahlAbstract:Periodic Crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated Crystals are a subset of aperiodic Crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and require q vectors for processing. Incommensurately modulated biological Macromolecular Crystals have been frequently observed but so far have not been solved. The authors of this article have been spearheading an initiative to determine this type of Crystal structure. The first step toward structure solution is to collect the diffraction data making sure that the satellite reflections are well separated from the main reflections. Once collected they can be integrated and then scaled with appropriate software. Then the assignment of the superspace group is needed. The most common form of modulation is in only one extra direction and can be described with a (3 + 1)D superspace group. The (3 + 1)D superspace groups for chemical Crystallographers are fully described in Volume C of International Tables for Crystallography. This text includes all types of Crystallographic symmetry elements found in small-molecule Crystals and can be difficult for structural biologists to understand and apply to their Crystals. This article provides an explanation for structural biologists that includes only the subset of biological symmetry elements and demonstrates the application to a real-life example of an incommensurately modulated protein Crystal.
-
How to assign a (3 + 1)-dimensional superspace group to an incommensurately modulated biological Macromolecular Crystal.
Journal of applied crystallography, 2017Co-Authors: Jason Porta, Jeff Lovelace, Gloria E. O. BorgstahlAbstract:Periodic Crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated Crystals are a subset of aperiodic Crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and require q vectors for processing. Incommensurately modulated biological Macromolecular Crystals have been frequently observed but so far have not been solved. The authors of this article have been spearheading an initiative to determine this type of Crystal structure. The first step toward structure solution is to collect the diffraction data making sure that the satellite reflections are well separated from the main reflections. Once collected they can be integrated and then scaled with appropriate software. Then the assignment of the superspace group is needed. The most common form of modulation is in only one extra direction and can be described with a (3 + 1)D superspace group. The (3 + 1)D superspace groups for chemical Crystallographers are fully described in Volume C of International Tables for Crystallography. This text includes all types of Crystallographic symmetry elements found in small-molecule Crystals and can be difficult for structural biologists to understand and apply to their Crystals. This article provides an explanation for structural biologists that includes only the subset of biological symmetry elements and demonstrates the application to a real-life example of an incommensurately modulated protein Crystal.
-
Macromolecular Crystal Quality
2013Co-Authors: Edward H. Snell, Henry D. Bellamy, Gloria E. O. BorgstahlAbstract:Publisher Summary This chapter discusses the Macromolecular Crystal quality. The chapter discusses the effect of internal order (or the lack of it) on the Crystals diffraction properties. The internal order of a Crystal can be characterized by a correlation length—that is, the distance over which all the atoms in the unit cells are “accurately” related by the Crystal-symmetry operators. The internal order of a Crystal can be characterized by a correlation length—that is, the distance over which all the atoms in unit cells are “accurately” related by the Crystal-symmetry operators. The chapter explores that the meaning of “accurately” depends on the resolution; one can see that the correlation length, the accuracy of Crystal repetitions, and the resolution of a reflection are all related. Therefore, as resolution increases (d-spacing decreases) the effective correlation length decreases and the number of unit cells contributing coherently to the diffraction decreases. Moreover, random disorder between the adjacent unit cells, a short-scale property in real space is seen as a global, resolution-dependent reduction in diffracted intensity in reciprocal space. Thus, careful measurements of the diffraction from Macromolecular Crystals can reveal the degree and nature of their disorder. Finally, this chapter concludes that a better understanding of the nature and causes of disorder in Macromolecular Crystals can lead to the production of better Crystals.
Jason Porta - One of the best experts on this subject based on the ideXlab platform.
-
How to assign a (3 + 1)-dimensional superspace group to an incommensurately modulated biological Macromolecular Crystal
Journal of Applied Crystallography, 2017Co-Authors: Jason Porta, Jeffrey J. Lovelace, Gloria E. O. BorgstahlAbstract:Periodic Crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated Crystals are a subset of aperiodic Crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and require q vectors for processing. Incommensurately modulated biological Macromolecular Crystals have been frequently observed but so far have not been solved. The authors of this article have been spearheading an initiative to determine this type of Crystal structure. The first step toward structure solution is to collect the diffraction data making sure that the satellite reflections are well separated from the main reflections. Once collected they can be integrated and then scaled with appropriate software. Then the assignment of the superspace group is needed. The most common form of modulation is in only one extra direction and can be described with a (3 + 1)D superspace group. The (3 + 1)D superspace groups for chemical Crystallographers are fully described in Volume C of International Tables for Crystallography. This text includes all types of Crystallographic symmetry elements found in small-molecule Crystals and can be difficult for structural biologists to understand and apply to their Crystals. This article provides an explanation for structural biologists that includes only the subset of biological symmetry elements and demonstrates the application to a real-life example of an incommensurately modulated protein Crystal.
-
How to assign a (3 + 1)-dimensional superspace group to an incommensurately modulated biological Macromolecular Crystal.
Journal of applied crystallography, 2017Co-Authors: Jason Porta, Jeff Lovelace, Gloria E. O. BorgstahlAbstract:Periodic Crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated Crystals are a subset of aperiodic Crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and require q vectors for processing. Incommensurately modulated biological Macromolecular Crystals have been frequently observed but so far have not been solved. The authors of this article have been spearheading an initiative to determine this type of Crystal structure. The first step toward structure solution is to collect the diffraction data making sure that the satellite reflections are well separated from the main reflections. Once collected they can be integrated and then scaled with appropriate software. Then the assignment of the superspace group is needed. The most common form of modulation is in only one extra direction and can be described with a (3 + 1)D superspace group. The (3 + 1)D superspace groups for chemical Crystallographers are fully described in Volume C of International Tables for Crystallography. This text includes all types of Crystallographic symmetry elements found in small-molecule Crystals and can be difficult for structural biologists to understand and apply to their Crystals. This article provides an explanation for structural biologists that includes only the subset of biological symmetry elements and demonstrates the application to a real-life example of an incommensurately modulated protein Crystal.
J M Harp - One of the best experts on this subject based on the ideXlab platform.
-
The well-tempered protein Crystal: annealing Macromolecular Crystals.
Methods in enzymology, 2003Co-Authors: B. Leif Hanson, J M Harp, G J BunickAbstract:Publisher Summary This chapter discusses about the annealing Macromolecular Crystals. Annealing techniques can overcome increased Crystal mosaicity after flash cooling. These techniques, involving the heating and cooling of a Crystal, can be referred to as annealing or tempering the Macromolecular Crystal. The term annealing implies a slow or gradual cooling of material after heating. There are several annealing techniques in use today. Macromolecular Crystal annealing (MCA) refers to the specific protocol that introduced the concept of annealing and that has been developed originally with Crystals of chromatin structural elements (nucleosome core particle). The Crystal is incubated in the buffer at either room temperature or the temperature at which the Crystal is grown. The single most important precondition for MCA is that the Crystal must be stable in the cryoprotectant during the period of incubation before the second flash cooling. The chapter presents the list of macromolecules for which annealing has been reported. Finally, this chapter elucidates the mode of action of annealing by explaining the results from the annealing experiments in terms of the mosaic-block model of the Crystals.
-
Macromolecular Crystal annealing: evaluation of techniques and variables.
Acta crystallographica. Section D Biological crystallography, 1999Co-Authors: J M Harp, B L Hanson, D E Timm, G J BunickAbstract:Additional examples of successful application of Macromolecular Crystal annealing are presented. A qualitative evaluation of variables related to the annealing process was conducted using a variety of Macromolecular Crystals to determine in which cases parameters may be varied and in which cases the original Macromolecular Crystal annealing protocol is preferred. A hypothesis is presented relating the solvent content of the Crystal to the specific protocol necessary for the successful application of annealing.
-
Macromolecular Crystal annealing: overcoming increased mosaicity associated with cryoCrystallography.
Acta Crystallographica Section D Biological Crystallography, 1998Co-Authors: J M Harp, D E Timm, G J BunickAbstract:Although cryogenic data collection has become the method of choice for Macromolecular Crystallography, the flash-cooling step can dramatically increase the mosaicity of some Crystals. Macromolecular Crystal annealing significantly reduces the mosaicity of flash-cooled Crystals without affecting molecular structure. The process, which cycles a flash-cooled Crystal to ambient temperature and back to cryogenic temperature, is simple, quick and requires no special equipment. The annealing process has been applied to Crystals of several different macromolecules grown from different precipitants and using a variety of cryoprotectants. The protocol for Macromolecular Crystal annealing also has been applied to restore diffraction from flash-cooled Crystals that were mishandled during transfer to or from cryogenic storage. These results will be discussed in relation to Crystal mosaicity and effects of radiation damage in flash-cooled Crystals.
