Protein Crystallizability

Abstract

Obtaining diffracting quality crystals remains a major challenge in protein structure research. We summarize and compare methods for selecting the best protein targets for crystallization, construct optimization and crystallization condition design. Target selection methods are divided into algorithms predicting the chance of successful progression through all stages of structural determination (from cloning to solving the structure) and those focusing only on the crystallization step. We tried to highlight pros and cons of different approaches examining the following aspects: data size, redundancy and representativeness, overfitting during model construction, and results evaluation. In summary, although in recent years progress was made and several sequence properties were reported to be relevant for crystallization, the successful prediction of protein crystallization behavior and selection of corresponding crystallization conditions continue to challenge structural researchers.

Can (We Make) Bacillus thuringiensis Crystallize More Than Its Toxins?

“…Several in vitro crystallization procedures have been developed to produce the high quantity of diffraction-grade microcrystals required for such an approach [ 10 ]. However, establishing reliable and reproducible procedures remains a laborious process that is very demanding in term of manpower and time and has an unpredictable outcome [ 7 , 8 , 9 , 12 ]. In vivo crystallization has recently emerged as a sound alternative to produce the crystalline samples required for such experiments [ 24 , 35 , 124 ].…”

“…Crystals therefore hold the promise of multiple applications, from the most fundamental academic research purposes to the development of innovative biotechnological products [ 6 ]. However, the crystallization of macromolecules, and notably proteins, is a process hardly predictable due to the many parameters affecting the nucleation and growth of crystals [ 7 , 8 , 9 ]. Crystallization of proteins implies that they are intrinsically capable of sufficiently strong crystal packing interactions to retain order in the long range.…”

Integrative Modeling of a Sin3/HDAC Complex Sub-structure

“…Although solution NMR and crystallographic studies have provided valuable insight into the structure of components of macromolecular complexes, it is often challenging to determine the architecture of subunits as they are assembled into higher-order structures. Crystallographic studies are limited by the requirement that the molecules isolated can form rigid crystals suitable for structure determination 1 . In addition, NMR studies of larger proteins and protein complexes are hindered by the large number of NMR signals generated which cause spectral crowding 2 .…”

fDETECT webserver: fast predictor of propensity for protein production, purification, and crystallization

“…It was used to produce slightly over 90% of the currently available structures [1, 2] [source: www.rcsb.org]. However, these efforts suffer relatively low success rates ranging between 2 and 10% [3–5]. The low rates stem from cumulative attrition along the protein production and crystallization pipelines.…”

“…These tools predict propensity for protein production and structure determination directly from the protein sequences. While majority of them are focused on the prediction of propensity for the final, structure production step [5, 20–22], a few tools that offer a broader scope were developed recently. The first such tool, PPCpred [23], addresses prediction of success of the protein production, purification, crystallization, and diffraction-quality crystallization (the final structure determination step).…”