In situ proteolysis for protein crystallization and structure determination

Dong, Aiping; Xu, Xiaohui; Edwards, A.M.; Chang, Changsoo; Chruszcz, M.; Cuff, M.E.; Cymborowski, M.; Leo, Rosa Di; Egorova, O.; Evdokimova, E.; Filippova, E.V.; Gu, Jun; Guthrie, Jennifer L.; Ignatchenko, Alexandr; Joachimiak, Andrzej; Klostermann, Natalie R.; Kim, Young Chang; Korniyenko, Yuri; Minor, Władek; Que, Qiuni; Savchenko, Alexei; Skarina, T.; Tan, Kemin; Yakunin, Alexander F.; Yee, Adelinda; Yim, V.; Zhang, Rongguang; Zheng, Hong; Akutsu, Masato; Arrowsmith, C.H.; Avvakumov, G.V.; Bochkarev, A.; Dahlgren, Lars; Dhe‐Paganon, Sirano; Dimov, Svetoslav; Dombrovski, L.; Finerty, P.J.; Flodin, S.; Flores, Alex F. C.; Gräslund, S.; Hammerström, Martin; Herman, Michael; Hong, Bum Soo; Hui, Raymond; Johansson, Ida; Liu, Yongson; Nilsson, M.E.; Nedyalkova, L.; Nordlund, P.; Nyman, T.; Min, Jinrong; Ouyang, Hui; Park, Hee Won; Qi, Chao; Rabeh, Wael M.; Shen, Limin; Shen, Yang; Sukumard, Deepthi; Tempel, W.; Tong, Yufeng; Tresagues, Lionel; Vedadi, Masoud; Walker, John R.; Weigelt, J.; Welin, M.; Wu, Hong; Xiao, Ting; Zeng, Hong; Zhu, Haizhong

doi:10.1038/nmeth1118

Cited by 194 publications

(177 citation statements)

References 16 publications

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“…3a-3f; for crystal optimization data, see Table 2). This salvage rate compares favorably to published data from reductive methylation (Kim et al, 2008) and limited proteolysis (Dong et al, 2007). In two cases, high-quality diffraction was also generated from crystals grown from subsequent sittingdrop vapor-diffusion experiments (in one case, X-ray diffraction from the MPCS crystal was of slightly higher resolution and in one case diffraction from the MPCS crystal was of slightly lower resolution).…”

Section: Discussionsupporting

confidence: 76%

Nanovolume optimization of protein crystal growth using the microcapillary protein crystallization system

Gerdts

Stahl²,

Napuli

et al. 2010

J Appl Cryst

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The Microcapillary Protein Crystallization System (MPCS) is a microfluidic, plug-based crystallization technology that generates X-ray diffraction-ready protein crystals in nanolitre volumes. In this study, 28 out of 29 (93%) proteins crystallized by traditional vapor diffusion experiments were successfully crystallized by chemical gradient optimization experiments using the MPCS technology. In total, 90 out of 120 (75%) protein/precipitant combinations leading to initial crystal hits from vapor diffusion experiments were successfully crystallized using MPCS technology. Many of the resulting crystals produced high-quality X-ray diffraction data, and six novel protein structures that were derived from crystals harvested from MPCS CrystalCards are reported.

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Section: Discussionsupporting

confidence: 76%

Nanovolume optimization of protein crystal growth using the microcapillary protein crystallization system

Gerdts

Stahl²,

Napuli

et al. 2010

J Appl Cryst

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“…The limited resolution of data from the hexagonal crystal form resulted in difficulty in modeling of the ␤-strands and connecting loops, so in situ trypsin digestion/crystallization was performed to change the crystal packing (34). Trypsin was added to syringacin M (500 M) at a ratio of 1:200 on ice, immediately prior to the addition to the drop.…”

Section: Crystallization Of Syringacin M-initialmentioning

confidence: 99%

The Crystal Structure of the Lipid II-degrading Bacteriocin Syringacin M Suggests Unexpected Evolutionary Relationships between Colicin M-like Bacteriocins

Grinter

Roszak

Cogdell

et al. 2012

Journal of Biological Chemistry

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Background: Syringacin M is a colicin M-like bacteriocin from the plant-pathogenic species Pseudomonas syringae. Results: The receptor binding domain of syringacin M has unexpected structural homology to that of colicin M. Conclusion: Syringacin M and colicin M appear to have evolved directly from a common ancestor. Significance: Bacteriocins can evolve novel receptor specificities through diversifying selection.

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“…A potential benefit of more precisely defining the minimal folded core of protein domains is an improvement of the crystallizability of the target protein. [16][17][18][19] To demonstrate this, dsRBD-1A and 1B were subjected to a parallel crystallization assay using 576 solution conditions. The full-length dsRBD-1A construct showed crystal growth in only nine conditions whereas dsRBD-1B construct produced crystal leads in 56 conditions.…”

Section: Crystallizability Improvementmentioning

confidence: 99%

Parallel screening and optimization of protein constructs for structural studies

et al. 2009

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A major challenge in structural biology remains the identification of protein constructs amenable to structural characterization. Here, we present a simple method for parallel expression, labeling, and purification of protein constructs (up to 80 kDa) combined with rapid evaluation by NMR spectroscopy. Our approach, which is equally applicable for manual or automated implementation, offers an efficient way to identify and optimize protein constructs for NMR or X-ray crystallographic investigations.

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In situ proteolysis for protein crystallization and structure determination

Cited by 194 publications

References 16 publications

Nanovolume optimization of protein crystal growth using the microcapillary protein crystallization system

Nanovolume optimization of protein crystal growth using the microcapillary protein crystallization system

The Crystal Structure of the Lipid II-degrading Bacteriocin Syringacin M Suggests Unexpected Evolutionary Relationships between Colicin M-like Bacteriocins

Parallel screening and optimization of protein constructs for structural studies

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