Crystal Growth 101
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Crystal Growth 101 Solutions for Crystal Growth Table of Contents Pages 1 - 3 Introduction 4 - 6 Sample Preparation for Crystallization 7 - 14 Crystallization Screening 15 - 17 Sitting Drop Vapor Diffusion 18 - 19 Hanging Drop Vapor Diffusion 20 - 21 Microbatch Crystallization 22 - 23 Converting Vapor Diffusion to Microbatch 24 - 25 Microdialysis Crystallization 26 - 27 Viewing Crystallization Experiments 28 - 29 Salt or Protein Crystals 30 - 45 Optimization 46 - 47 Drop Ratio 48 - 49 Temperature as a Crystallization Variable 50 - 57 Seeding 58 - 59 Buffer Table 60 Buffer Formulation 61 Phosphate Buffer Dilution Table 62 Using Volatile Buffers to Adjust Drop pH and Induce Crystallization 63 - 68 Reagent Formulation and Handling 69 - 70 Solubility Table 71 Halides for Phasing 72 - 88 PEG Stability Hampton Research 34 Journey Aliso Viejo, CA 92656-3317 U.S.A. Tel: (949) 425-1321 • Fax: (949) 425-1611 Technical Support e-mail: [email protected] Website: hamptonresearch.com © 1991-2021 Hampton Research Corp. All rights reserved. Printed in the United States of America. This guide or parts thereof may not be reproduced in any form without the written permission of the publishers. Introduction Solutions for Crystal Growth Crystal Growth 101 page 1 Introduction to the Crystallization of Biological scientific problem. Instead, crystallization is often a matter of searching, as Macromolecules systematically as possible, through crystallization experiments, to identify The Crystal Growth 101 series prepared by Hampton Research presents an those variables key to success, as well as their ranges. Initially, one employs overview of the preparation of the sample, methods, screening, optimiza- crystallization screening, typically to identify a hit, an association of vari- tion, reagent formulation, and other aspects of protein crystallization. We ables that produces a crystal. In some instances this will produce crystals hope Crystal Growth 101 will prove a useful resource and inspiration in your with the desired characteristics. More often than not, a series of successive crystal quest. Best of success with your crystals! experiments, termed optimization, will need to be carried out, in order to produce crystals with the desired properties, be it for structural biology, puri- The First Protein Crystal & Beyond fication, formulation, or the delivery of a biological therapeutic. The first record of crystals of biological macromolecules were those of hemoglobin, reported by Hunefeld around 1840.1,2 During the 1880s, Table 1. crystallization moved from being a mere curiosity to a method for purifi- Biochemical & Chemical variables that could or do affect cation.3,4 During the 1920s and 1930s crystallization grew in popularity, protein crystal growth with the crystallization of insulin by John Jacob Abel and colleagues, as well Purity of the sample Genetic modifications as work by James B. Sumner, demonstrating enzymes could be obtained as Conformational flexibility of the crystalline proteins, alongside the work with a number of important crystal- Symmetry of the molecule line enzymes by John Northrop and colleagues.5-7 It was not until the late sample Stability and level of denaturation 1930s that crystalline proteins were introduced to X-rays, beginning a torrid Homogeneity of the sample affair that shines bright to this day.8 of the sample pH and buffer Isoelectric point Much has changed with how biological macromolecules are sourced. Early on, and to a small extent today, samples were obtained by protein chemists Type and concentration of the His tags and other purification through extraction and purification from natural sources, including plants, precipitant (reagent) tags – presence or absence as well as various organs and tissues of pigs, cows, and other animals. In Concentration of the sample Thermal stability the 1980s, with the near cataclysmic death of heavy metal and the fortuitous end of disco, geneticists and molecular biologist rose above the fog and hair Purity of the sample pH stability spray, allowing DNA technology to integrate with structural biology, totally accelerating and transforming the field of structural biology. Additives, co-factors, ligands, inhibitors, effectors, History of the sample It’s Simple, But Complicated and excipients Although much change, and the numerous advancements in molecular Chaotropes Proteolysis biology and crystallography has reduced many of the arduous, laborious, math and physics infused tasks to, in some cases, the mere push of a but- Detergents Microbial contamination ton, crystallization remains at the crossroads where science meets art. The growth and optimization of crystals of biological macromolecules remains Metals Storage of the sample largely empirical in nature. There is no comprehensive theory to guide ef- forts and experiments related to the crystallization of proteins, nucleic ac- Handling of the sample and Ionic strength ids, and other biological macromolecules. Although much knowledge and associate cleanliness experience has been accumulated, the crystallization of a protein involves Anion and cation type and Reducing or oxidizing agents collected wisdom, intuition, creativity, patience, and perseverance. concentration Degree of relative Source of the sample Crystallization of biological macromolecules composed of many thousands supersaturation of different atoms, bound together with many degrees of freedom, is a com- Presence of amorphous or Initial and final concentration of plex task. Confounding this many variables and factors influencing the particulate material the reagent 9-11 Post-translational crystallization experiment (Tables 1 & 2). Path and rate of equilibration modifications This extensive number of variables confounded with typically limited sam- Chemical modifications ple material negates a precise and reasoned strategy typically applied to a 1 Introduction Solutions for Crystal Growth Crystal Growth 101 page 2 Table 2. Physical variables that could or do affect Alas, there is much more to crystallization than making, formulation, or protein crystal growth buying and using tools. So before heading off to grab a pipette or pressing Temperature Electric and magnetic fields go on the robot, consider some important principles as a foundation of your crystallization strategy, as presented originally by the giant of crystallization, Surface of the crystallization Rate of equilibration 12-13 device Alex McPherson. Method of crystallization Viscosity of the reagent The Sample Gravity, convection, and Heterogeneous and epitaxial sedimentation nucleants The sample is the most important variable in the crystallization experiment. Prepare, purify, handle, and store the sample with only the greatest care and Geometry of crystallization Vibration and sound device respect. Manipulate the sample and refine its environment (buffer, reagent) as needed to produce the desired crystals. Volume of the sample and Time reagent Homogeneity Pressure Dielectric property of the reagent Purify, purify, then purify some more. Start with a pure, uniform population of the sample. Despite the largely empirical nature of crystallization, today’s crystal grower may choose from a readily available collection of screens, plates, and tools Solubility for identifying initial crystallization conditions. These tools are accom- Solubilize the sample in a sample buffer that is optimized with regard to panied by a portfolio of methods (Table 3), screens, and reagents (Table pH, buffer, and excipients that dissolve the sample to high concentration 4) for crystal optimization. These tool chests, together with a rich pool of free of aggregates, precipitate, or other phases. Pursue monodispersity not crystallization literature to explore, along with a caring and sharing group polydispersity. of mentors and instructors offering wisdom and advice through meetings, workshops, and the internet, provide a tremendous resource for today’s crys- Stability tal grower. Prepare and maintain the sample in a chemical and physical solution that promotes optimal stability of the sample. Do not allow the sample to go to Table 3. Crystallization Methods – Achieving the dark side, form oligomers, undergo significant conformational change, Supersaturation denature or change in any way before and during crystallization. Pursue a Vapor Diffusion stable and unchanging sample. Sequential Extraction (Sitting, Hanging, Sandwich) Batch Supersaturation pH Induced (Microbatch with or without oil) Find and pursue ways to move the sample into a supersaturated state. Using Dialysis (Microdialysis) Temperature Induced reagents, pH, temperature, and other variables to move sample equilibrium Free interface diffusion from a solution to a solid. Effector Addition (Silver Bullet) (Counter diffusion, liquid bridge) Controlled Evaporation Association Promote the orderly association of the sample molecules while avoiding Table 4. Examples of reagents used in protein non-specific aggregation, precipitate, or phase separation. Manipulate the crystallization chemical and physical environment to facilitate positive molecular interac- Salts (Ammonium sulfate, Sodium Non-Volatile Organics tions. formate, Ammonium (+/-)-2-Methyl-2,4-pentanediol, phosphate…) Glycerol, 1,6-Hexanediol…) Nucleation Polymers (Polyethylene glycols Promote and induce a few nuclei in a controlled manner. The number, size, Buffers (HEPES, Tris, Sodium (M 200 – 20,000), Ethylene r acetate, MES…) and quality of the crystal depend upon the first nuclei and the mechanism imine,