Protein Structure Validation and Analysis with X-Ray Crystallography

Abstract

X-ray crystallography is the main technique for the determination of protein structures. About 85 % of all protein structures known to date have been elucidated using X-ray crystallography. Knowledge of the three-dimensional structure of proteins can be used in various applications in biotechnology, biomedicine, drug design, and basic research and as a validation tool for protein modifications, ligand binding, and structural authenticity. Moreover, the requirement for pure, homogeneous, and stable protein solutions in crystallizations makes X-ray crystallography beneficial in other fields of protein research as well. Here, we describe the technique of X-ray protein crystallography and the steps involved for a successful three-dimensional crystal structure determination.

Rapid 3-dimensional shape determination of globular proteins by mobility capillary electrophoresis and native mass spectrometry

“…Biophysical methods such as X-ray crystallography, [4][5][6][7] nuclear magnetic resonance (NMR), [8][9][10] and electron microscopy [11][12][13] could provide detailed structural information of proteins but require laborious sample preparation, and the analysis of heterogeneous mixtures remains challenging. [14][15][16][17][18] Nanopores and nanopipettes have also been developed to analyze the volume, surface charge and structure dynamic process of proteins. [19][20][21][22] New approaches capable of providing complementary protein structure information and rapid-in-analysis are demanded to bridge the gap between high-throughput proteomics and structural biology.…”

Characterizing metal-binding sites in proteins with X-ray crystallography

“…The crystal structures of iron-containing hemoglobin (PDB ID: 1FDH) 21 and manganese- and calcium-containing concanavalin A (PDB ID: 2CNA) 22 are among the earliest structures deposited in the Protein Data Bank (PDB) 23 . Thereafter, many manuscripts and book chapters regarding the expression and purification of metal-containing proteins, handling of metals with more than one oxidation state, crystallization, data collection of metal-containing crystals, and validation of protein-metal binding environments were published 15,20,24–37 . To our knowledge, however, there are currently no publications that gather this information into a clear, easy to use, step-wise protocol.…”

Biophysical, Biochemical, and Cell Based Approaches Used to Decipher the Role of Carbonic Anhydrases in Cancer and to Evaluate the Potency of Targeted Inhibitors

“…X-ray crystallography remains the most effective way to determine atomic models of proteins and nucleic acids [ 98 ]. It has become invaluable in the field of targeted drug design and for the determination of atomic and molecular structure of protein crystals [ 99 ].…”