2007
DOI: 10.1110/ps.072914007
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Toward rational protein crystallization: A Web server for the design of crystallizable protein variants

Abstract: Growing well-diffracting crystals constitutes a serious bottleneck in structural biology. A recently proposed crystallization methodology for ''stubborn crystallizers'' is to engineer surface sequence variants designed to form intermolecular contacts that could support a crystal lattice. This approach relies on the concept of surface entropy reduction (SER), i.e., the replacement of clusters of flexible, solvent-exposed residues with residues with lower conformational entropy. This strategy minimizes the loss … Show more

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Cited by 259 publications
(258 citation statements)
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“…A slightly smaller complex, Cog5 99-387 -Cog7 5-80 , crystallized under a wider range of solution conditions, with the best crystals diffracting X-rays to 9-Å resolution. These crystals were further improved through the use of surface entropy reduction (27); ultimately, the best crystals were obtained by changing seven nonconserved residues (five Glu and two Gln) predicted to be located on flexible loops to Ala (SI Materials and Methods). The structure was determined by using multiwavelength anomalous diffraction (MAD).…”
Section: Significancementioning
confidence: 99%
“…A slightly smaller complex, Cog5 99-387 -Cog7 5-80 , crystallized under a wider range of solution conditions, with the best crystals diffracting X-rays to 9-Å resolution. These crystals were further improved through the use of surface entropy reduction (27); ultimately, the best crystals were obtained by changing seven nonconserved residues (five Glu and two Gln) predicted to be located on flexible loops to Ala (SI Materials and Methods). The structure was determined by using multiwavelength anomalous diffraction (MAD).…”
Section: Significancementioning
confidence: 99%
“…Because the initial crystallization attempts did not lead to diffracting crystals, the VP14 sequence was analyzed using the Surface-EntropyReduction prediction (SERp) server (Goldschmidt et al, 2007). The program predicted Lys-381 and Glu-382 to be in loop regions of the protein and recommended mutation of these residues to Ala to improve the possibility of crystal contacts.…”
Section: Surface Site Mutagenesis For Ke381aamentioning
confidence: 99%
“…[26][27][28] The SER method typically replaces solvent-exposed, flexible amino acids, such as Lys, Glu, and Gln, with less flexible residues, such as Ala. It has been successfully used for several protein targets, [29][30][31] and a web-based server has been created to suggest suitable mutation sites in any given protein sequence. 30 Synthetic symmetrization involves introducing into the surface of a protein specific motifs likely to drive symmetric self-association.…”
Section: Introductionmentioning
confidence: 99%
“…It has been successfully used for several protein targets, [29][30][31] and a web-based server has been created to suggest suitable mutation sites in any given protein sequence. 30 Synthetic symmetrization involves introducing into the surface of a protein specific motifs likely to drive symmetric self-association. Motivation for the approach derives in part from the observation that protein oligomers tend to crystallize in space groups that support the point group symmetry of the oligomer.…”
Section: Introductionmentioning
confidence: 99%