Biological Macromolecular Crystals Research Articles

Berkeley Screen: a set of 96 solutions for general macromolecular crystallization.

Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography program at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens.

How to assign a (3 + 1)-dimensional superspace group to an incommensurately modulated biological macromolecular crystal.

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.

Efficient calculation of diffracted intensities in the case of nonstationary scattering by biological macromolecules under XFEL pulses.

The calculation of diffracted intensities from an atomic model is a routine step in the course of structure solution, and its efficiency may be crucial for the feasibility of the study. An intense X-ray free-electron laser (XFEL) pulse can change the electron configurations of atoms during its action. This results in time-dependence of the diffracted intensities and complicates their calculation. An algorithm is suggested that enables this calculation with a computational cost comparable to that for the time-independent case. The intensity is calculated as a sum of the `effective' intensity and a finite series of `correcting' intensities. These intensities are calculated in the conventional way but with modified atomic scattering factors that are specially derived for a particular XFEL experiment. The total number of members of the series does not exceed the number of chemically different elements present in the object under study. This number is small for biological molecules; in addition, the correcting terms are negligible within the parameter range and accuracy acceptable in biological crystallography. The time-dependent atomic scattering factors were estimated for different pulse fluence levels by solving the system of rate equations. The simulation showed that the changes in a diffraction pattern caused by the time-dependence of scattering factors are negligible if the pulse fluence does not exceed the limit that is currently achieved in experiments with biological macromolecular crystals (10(4) photons Å(-2) per pulse) but become significant with an increase in the fluence to 10(6) or 10(8) photons Å(-2) per pulse.

The interaction of sweet potato amylose/amylopectin and KCl during drying

Sweet potato amylose and amylopectin were isolated from retrograded sweet potato starch. During isolation, the retrograded starches were resolved in 4.0 M KOH and then 4.0 M HCl was added to adjust the pH of the solutions to neutral, therefore KCl was formed in starch solutions. Long or short crystals of KCl grew on sweet potato amylose solution or amylopectin solution in the drying process. The results of IR, NMR, XRD, DSC and SEM of corresponding samples suggest that the attraction of amylose or amylopectin to KCl leads to the formation of snowflake crystals. The shape of KCl crystals growing in starch solutions acts more like biological macromolecular crystals than that of inorganic salt. Amylose promotes the growth of KCl crystals, while amylopectin inhibits it. The different up and down field of C-6 signals in NMR indicates the different link pattern of starch with KCl salt. In the course of crystallization, sweet potato starch grows into B-type crystal, with the characteristic strongest peak located at 17°. KCl is entrapped by starch in the crystallization progress during starch drying. The findings in the paper provide an insight into the interaction between starch and salts.

13th International Conference on the Crystallization of Biological Macromolecules (ICCBM13) Proceedings Overview

This overview offers a context for the individual articles published in the ICCBM13 virtual special issue of Crystal Growth & Design, a historical perspective, and our opinions on what the future may hold for biological macromolecular crystallization.

The Biomolecular Crystallization Database Version 4: expanded content and new features

The Biological Macromolecular Crystallization Database (BMCD) has been a publicly available resource since 1988, providing a curated archive of information on crystal growth for proteins and other biological macromolecules. The BMCD content has recently been expanded to include 14 372 crystal entries. The resource continues to be freely available at http://xpdb.nist.gov:8060/BMCD4. In addition, the software has been adapted to support the Java-based Lucene query language, enabling detailed searching over specific parameters, and explicit search of parameter ranges is offered for five numeric variables. Extensive tools have been developed for import and handling of data from the RCSB Protein Data Bank. The updated BMCD is called version 4.02 or BMCD4. BMCD4 entries have been expanded to include macromolecule sequence, enabling more elaborate analysis of relations among protein properties, crystal-growth conditions and the geometric and diffraction properties of the crystals. The BMCD version 4.02 contains greatly expanded content and enhanced search capabilities to facilitate scientific analysis and design of crystal-growth strategies.

Phase sensitive x-ray diffraction imaging of defects in biological macromolecular crystals.

Conventional x-ray diffraction topography is currently used to map defects in the bulk of protein crystals, but the lack of sufficient contrast is frequently a limiting factor. We experimentally demonstrate that this barrier can be circumvented using a method that combines phase sensitive and diffraction imaging principles. Details of defects revealed in tetragonal lysozyme and cubic ferritin crystals are presented and discussed. The approach enabling the detection of the phase changes of diffracted x rays should prove to be useful in the study of defect structures in a broad range of biological macromolecular crystals.

Statistical methods for the objective design of screening procedures for macromolecular crystallization.

The crystallization of a new macromolecule is still very much a trial-and-error process. As is well known, it requires the search of a large parameter space of experimental settings to find the relatively few idiosyncratic conditions that lead to diffraction-quality crystals. Crystallographers have developed a variety of screens to help identify initial crystallization conditions, including those based on systematic grids, incomplete factorial and sparse-matrix approaches. These are somewhat subjectively formulated based on accumulated data from past crystallization experiments. Ideally, one would prefer as objective a procedure as possible; however, that requires objective methods that incorporate a broad source of crystallization data. The Biological Macromolecular Crystallization Database (BMCD), a repository of all published crystallization conditions, is an obvious source of this data. This database has been augmented with a hierarchical classification of the macromolecules contained in the BMCD as well as extensive data on the additives used with them. A statistical analysis of the augmented BMCD shows the existence of significant correlations between families of macromolecules and the experimental conditions under which they crystallize. This in turn leads to a Bayesian technique for determining the probability of success of a set of experimental conditions based on the data in the BMCD as well as facts about a macromolecule known prior to crystallization. This has been incorporated into software that enables users to rank experimental conditions for new macromolecules generated by a dense partial factorial design. Finally, an additional advantage of the software described here is that it also facilitates the accumulation of the data required for improving the accuracy of estimation of the probabilities of success - knowledge of the conditions which lead to failure of crystallization.

Cryogenic mounting, archiving and transportation of biological macromolecular crystals

Cryogenic mounting, archiving and transportation of biological macromolecular crystals

放射光利用によるタンパク質の結晶構造解析 多波長異常分散法の利用

Synchrotron radiation (SR) is an extremely useful X-ray source for protein crystallography. It is high brilliance, high intensity and small divergence white X-ray source, which enables us to collect high resolution diffraction data of biological macromolecular crystals with large cell dimensions. Furthermore, wavelength tunability of SR is essential for the phase determination by multiwavelength anomalous diffraction (MAD) method, which has a possibility of the direct phase determination of metal proteins, selenomethionyl proteins and proteins with single isomorphous derivative of poor isomorphism.MAD method is applied for the structure determination of cytochrome c-553 from Desulfovibrio vulgaris Miyazaki F strain.

THE PROBLEM OF AMBIGUITY IN PATTERSON ANALYSIS TREATED BY DIRECT METHOD

In crystal structure determination with presence of heavy atoms, Patterson method and methods based on it, i.e. the heary atom method, the isomorphous replacement method and the anomalous scattering method are conventionally employed. When applying these methods ambiguities in results often arise. It had been suggested by one of the present authors in 1965 that the ambiguities can be eliminated by using the direct method. In recent years, similar investigations are continued abroad. These methods not only present their distinctive feathures in the work of structure analysis of crystals of small molecules, but their further developements will be effec-tive in extension the field of application of direct methods in structure analysis of biological macro-molecular crystals, making contribution on improving the state of art of these studies. The application of the method in the case of centric symmetry have been demonstrated in the published work of one of the present authors. Another successful example on the case of non-centric symmetry is given here. Although only the problem of ambiguity of Patterson method is treated in this example, but the same approach can be applied to that of the isomorphous replacement method and the anomalous scattering method.