Now we’re cooking: new successes for shake-and-bake

Ealick, S.E.

doi:10.1016/s0969-2126(97)00203-7

Cited by 8 publications

(5 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The structure determination of [Tyr 15 ]EpI, with a total of 284 non-hydrogen atoms in the asymmetric unit, represents one of the largest, previously unsolved, structures determined by direct methods (45). However, this was not a straightforward process.…”

Section: Discussionmentioning

confidence: 99%

The 1.1 Å Resolution Crystal Structure of [Tyr¹⁵]EpI, a Novel α-Conotoxin fromConus episcopatus, Solved by Direct Methods

Loughnan

Miller

et al. 1998

Biochemistry

View full text Add to dashboard Cite

Conotoxins are valuable probes of receptors and ion channels because of their small size and highly selective activity. alpha-Conotoxin EpI, a 16-residue peptide from the mollusk-hunting Conus episcopatus, has the amino acid sequence GCCSDPRCNMNNPDY(SO3H)C-NH2 and appears to be an extremely potent and selective inhibitor of the alpha3beta2 and alpha3beta4 neuronal subtypes of the nicotinic acetylcholine receptor (nAChR). The desulfated form of EpI ([Tyr15]EpI) has a potency and selectivity for the nAChR receptor similar to those of EpI. Here we describe the crystal structure of [Tyr15]EpI solved at a resolution of 1.1 A using SnB. The asymmetric unit has a total of 284 non-hydrogen atoms, making this one of the largest structures solved de novo by direct methods. The [Tyr15]EpI structure brings to six the number of alpha-conotoxin structures that have been determined to date. Four of these, [Tyr15]EpI, PnIA, PnIB, and MII, have an alpha4/7 cysteine framework and are selective for the neuronal subtype of the nAChR. The structure of [Tyr15]EpI has the same backbone fold as the other alpha4/7-conotoxin structures, supporting the notion that this conotoxin cysteine framework and spacing give rise to a conserved fold. The surface charge distribution of [Tyr15]EpI is similar to that of PnIA and PnIB but is likely to be different from that of MII, suggesting that [Tyr15]EpI and MII may have different binding modes for the same receptor subtype.

show abstract

Section: Discussionmentioning

confidence: 99%

The 1.1 Å Resolution Crystal Structure of [Tyr¹⁵]EpI, a Novel α-Conotoxin fromConus episcopatus, Solved by Direct Methods

Loughnan

Miller

et al. 1998

Biochemistry

View full text Add to dashboard Cite

show abstract

“…Three α-conotoxin crystal structures have now been determined: GI (), PnIA (), and now PnIB. All three structures were determined by Shake-and-Bake direct methods ( , ), showing that it is a generally applicable method for solving crystal structures of this class. We have found, that for α-conotoxin structures, the important requirement for structure determination by this method is the availability of high-resolution data.…”

Section: Discussionmentioning

confidence: 99%

Crystal Structure at 1.1 Å Resolution of α-Conotoxin PnIB: Comparison with α-Conotoxins PnIA and GI

Gehrmann

Alewood

et al. 1997

Biochemistry

View full text Add to dashboard Cite

Conotoxins are small, cysteine-rich peptides isolated from the venom of Conus spp. of predatory marine snails, which selectively target specific receptors and ion channels critical to the functioning of the neuromuscular system. alpha-Conotoxins PnIA and PnIB are both 16-residue peptides (differing in sequence at only two positions) isolated from the molluscivorous snail Conus pennaceus. In contrast to the muscle-selective alpha-conotoxin GI from Conus geographus, PnIA and PnIB block the neuronal nicotinic acetylcholine receptor (nAChR). Here, we describe the crystal structure of PnIB, solved at a resolution of 1.1 A and phased using the Shake-and-Bake direct methods program. PnIB crystals are orthorhombic and belong to the space group P212121 with the following unit cell dimensions: a = 14.6 A, b = 26.1 A, and c = 29.2 A. The final refined structure of alpha-conotoxin PnIB includes all 16 residues plus 23 solvent molecules and has an overall R-factor of 14.7% (R-free of 15.9%). The crystal structures of the alpha-conotoxins PnIB and PnIA are solved from different crystal forms, with different solvent contents. Comparison of the structures reveals them to be very similar, showing that the unique backbone and disulfide architecture is not strongly influenced by crystal lattice constraints or solvent interactions. This finding supports the notion that this structural scaffold is a rigid support for the presentation of important functional groups. The structures of PnIB and PnIA differ in their shape and surface charge distribution from that of GI.

show abstract

“…Traditionally, common phasing techniques require search templates that share sufficiently high structural similarity in molecular replacement (Rossmann, 2001) or the introduction of heavy atoms in isomorphous replacement (Green et al, 1954) and anomalous scattering (Hendrickson, 1991). The structures of small-molecule crystals can be determined ab initio via the direct method, which is a very effective tool (Ealick, 1997;Weeks & Miller, 1999;Sheldrick, 2008). Since the direct method is restricted to structures with small molecular weight and very high diffraction resolution (1.2 A ˚or better), it is not generally applicable to macromolecular crystals.…”

Section: Introductionmentioning

confidence: 99%

Direct phasing algorithm for protein crystals with high solvent content using low-resolution diffraction data

Jiang

Miao

Pan

et al. 2023

Acta Cryst Sect D Struct Biol

View full text Add to dashboard Cite

Over the past decade, iterative projection algorithms, an effective approach to recovering phases from a single intensity measurement, have found application in protein crystallography to directly surmount the `phase problem'. However, previous studies have always assumed that some prior knowledge constraints (i.e. a low-resolution envelope about the protein structure in the crystal cell or histogram matching requiring a similar density distribution to the target crystal) must be known for successful phase retrieval, thus hindering its widespread application. In this study, a novel phase-retrieval workflow is proposed that eliminates the need for a reference density distribution by utilizing low-resolution diffraction data in phasing algorithms. The approach involves randomly assigning one out of 12 possible phases at 30° intervals (or two for centric reflections) to produce an initial envelope, which is then refined through density modification after each run of phase retrieval. To evaluate the success of the phase-retrieval procedure, information entropy is introduced as a new metric. This approach was validated using ten protein structures with high solvent content, demonstrating its effectiveness and robustness.

show abstract

Now we’re cooking: new successes for shake-and-bake

Cited by 8 publications

References 24 publications

The 1.1 Å Resolution Crystal Structure of [Tyr¹⁵]EpI, a Novel α-Conotoxin fromConus episcopatus, Solved by Direct Methods

The 1.1 Å Resolution Crystal Structure of [Tyr¹⁵]EpI, a Novel α-Conotoxin fromConus episcopatus, Solved by Direct Methods

Crystal Structure at 1.1 Å Resolution of α-Conotoxin PnIB: Comparison with α-Conotoxins PnIA and GI

Direct phasing algorithm for protein crystals with high solvent content using low-resolution diffraction data

Contact Info

Product

Resources

About

Now we’re cooking: new successes for shake-and-bake

Cited by 8 publications

References 24 publications

The 1.1 Å Resolution Crystal Structure of [Tyr15]EpI, a Novel α-Conotoxin fromConus episcopatus, Solved by Direct Methods

The 1.1 Å Resolution Crystal Structure of [Tyr15]EpI, a Novel α-Conotoxin fromConus episcopatus, Solved by Direct Methods

Crystal Structure at 1.1 Å Resolution of α-Conotoxin PnIB: Comparison with α-Conotoxins PnIA and GI

Direct phasing algorithm for protein crystals with high solvent content using low-resolution diffraction data

Contact Info

Product

Resources

About

The 1.1 Å Resolution Crystal Structure of [Tyr¹⁵]EpI, a Novel α-Conotoxin fromConus episcopatus, Solved by Direct Methods

The 1.1 Å Resolution Crystal Structure of [Tyr¹⁵]EpI, a Novel α-Conotoxin fromConus episcopatus, Solved by Direct Methods