Revealing protein structures: crystallization of protein-ligand complexes - co-crystallization and crystal soaking

. 2025 Apr ; 15 (4) : 542-550. [epub] 20241020

Jazyk angličtina Země Anglie, Velká Británie Médium print-electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid39428257

Grantová podpora
PC24-047 Federation of European Biochemical Societies
101137229 HORIZON EUROPE Research Infrastructures

Protein crystallogenesis represents a key step in X-ray crystallography studies that employ co-crystallization and ligand soaking for investigating ligand binding to proteins. Co-crystallization is a method that enables the precise determination of binding positions, although it necessitates a significant degree of optimization. The utilization of microseeding can facilitate a reduction in sample requirements and accelerate the co-crystallization process. Ligand soaking is the preferred method due to its simplicity; however, it requires careful control of soaking conditions to ensure the successful integration of the ligands. This research protocol details the procedures for co-crystallization and soaking to achieve protein-ligand complex formation, which is essential for advancing drug discovery. Additionally, a simple protocol for demonstrating soaking for educational purposes is described.

Zobrazit více v PubMed

Wienen‐Schmidt B, Oebbeke M, Ngo K, Heine A and Klebe G (2021) Two methods, one goal: structural differences between cocrystallization and crystal soaking to discover ligand binding poses. ChemMedChem 16, 292–300. PubMed PMC

Erlanson DA, Fesik SW, Hubbard RE, Jahnke W and Jhoti H (2016) Twenty years on: the impact of fragments on drug discovery. Nat Rev Drug Discov 15, 605–619. PubMed

Danley DE (2006) Crystallization to obtain protein‐ligand complexes for structure‐aided drug design. Acta Crystallogr D 62, 569–575. PubMed

Chilingaryan Z, Yin Z and Oakley AJ (2012) Fragment‐based screening by protein crystallography: successes and pitfalls. Int J Mol Sci 13, 12857–12879. PubMed PMC

Hassell AM, An G, Bledsoe RK, Bynum JM, Carter HL, Deng SJJ, Gampe RT, Grisard TE, Madauss KP, Nolte RT et al. (2006) Crystallization of protein‐ligand complexes. Acta Crystallogr D 63, 72–79. PubMed PMC

Müller I (2017) Guidelines for the successful generation of protein‐ligand complex crystals. Acta Crystallogr D 73, 79–92. PubMed PMC

Stewart L, Clark R and Behnke C (2002) High‐throughput crystallization and structure determination in drug discovery. Drug Discov Today 7, 187–196. PubMed

Hoeppner A, Schmitt L and Smits HJS (2013) Proteins and their ligands: their importance and how to crystallize them. In Advanced Topics on Crystal Growthpp. 3–42. InTechOpen, Rijeka.

Oswald C, Smits SHJ, Bremer E and Schmitt L (2008) Microseeding – a powerful tool for crystallizing proteins complexed with hydrolyzable substrates. Int J Mol Sci 9, 1131–1141. PubMed PMC

Benvenuti M and Mangani S (2007) Crystallization of soluble proteins in vapor diffusion for x‐ray crystallography. Nat Protoc 2, 1633–1651. PubMed

Matthews BW (1974) Determination of molecular weight from protein crystals. J Mol Biol 82, 513–526. PubMed

Schmidt M (2013) Mix and inject: reaction initiation by diffusion for time‐resolved macromolecular crystallography. Adv Condens Matter Phys 2013. doi: 10.1155/2013/167276 DOI

Singh O, Shillings A, Craggs P, Wall I, Rowland P, Skarzynski T, Hobbs CI, Hardwick P, Tanner R, Blunt M et al. (2013) Crystal structures of ASK1‐inhibtor complexes provide a platform for structure‐based drug design. Protein Sci 22, 1071–1077. PubMed PMC

Stum EA and Gleichmann T (1999) Soaking techniques. In Crystallization of Nucleic Acids and Proteins: A Practical Approach (Ducruix A and Giegé R, eds), 2nd edn, Oxford Academic, Oxford. doi: 10.1093/oso/9780199636792.003.0017 DOI

Ballone A, Lau RA, Zweipfenning FPA and Ottmann C (2020) A new soaking procedure for X‐ray crystallographic structural determination of protein‐peptide complexes. Acta Crystallogr F 76, 501–507. PubMed PMC

Niesen FH, Berglund H and Vedadi M (2007) The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat Protoc 2, 2212–2221. PubMed

Dale GE, Oefner C and D'Arcy A (2003) The protein as a variable in protein crystallization. J Struct Biol 142, 88–97. PubMed

Dessau MA and Modis Y (2010) Protein crystallization for X‐ray crystallography. J Vis Exp 9, 1–6. PubMed PMC

Teplitsky E, Joshi K, Ericson DL, Scalia A, Mullen JD, Sweet RM and Soares AS (2015) High throughput screening using acoustic droplet ejection to combine protein crystals and chemical libraries on crystallization plates at high density. J Struct Biol 191, 49–58. PubMed

Ng JT, Dekker C, Reardon P and von Delft F (2016) Lessons from ten years of crystallization experiments at the SGC. Acta Crystallogr D 72, 224–235. PubMed PMC

D'Arcy A, Bergfors T, Cowan‐Jacob SW and Marsh M (2014) Microseed matrix screening for optimization in protein crystallization: what have we learned? Acta Crystallogr F 70, 1117–1126. PubMed PMC

Garman EF and Doublié S (2003) [11] Cryocooling of macromolecular crystals: optimization methods. Methods Enzymol 368, 188–216. PubMed

Eckert K, Ernst HA, Schneider E, Larsen S and Lo Leggio L (2003) Crystallization and preliminary X‐ray analysis of Alicyclobacillus acidocaldarius endoglucanase CelA. Acta Crystallogr D 59, 139–141. PubMed

McPherson A, Malkin AJ, Kuznetsov YG and Koszelak S (1996) Incorporation of impurities into macromolecular crystals. J Cryst Growth 168, 74–92.

Luft JR, Wolfley JR, Said MI, Nagel RM, Lauricella AM, Smith JL, Thayer MH, Veatch CK, Snell EH, Malkowski MG et al. (2007) Efficient optimization of crystallization conditions by manipulation of drop volume ratio and temperature. Protein Sci 16, 715–722. PubMed PMC

Krengel U and Imberty A (2007) Crystallography and lectin structure database. In Lectins: Analytical Technologies (Nilsson CL, ed.), pp. 15–50. Elsevier, Amsterdam.

Sauter C, Balg C, Moreno A, Dhouib K, Théobald‐Dietrich A, Chênevert R, Giegé R and Lorber B (2009) Agarose gel facilitates enzyme crystal soaking with a ligand analog. J Appl Cryst 42, 279–283.

Lorber B, Sauter C, Théobald‐Dietrich A, Moreno A, Schellenberger P, Robert MC, Capelle B, Sanglier S, Potier N and Giegé R (2009) Crystal growth of proteins, nucleic acids, and viruses in gels. Prog Biophys Mol Biol 101, 13–25. PubMed

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...