Efficient anisotropic refinement of macromolecular structures using FFT

Murshudov, Garib N.; Vagin, A.A.; Лебедев, А. А.; Wilson, K.S.; Dodson, E.J.

doi:10.1107/s090744499801405x

Cited by 1,022 publications

(875 citation statements)

References 18 publications

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“…30 Structures were solved by molecular replacement using PHASER 31 and homologous models obtained from the PDB. Crystallographic models were rebuilt using O 32 or COOT 33 and refinement was performed using REFMAC5 34 or PHENIX. 35 …”

Section: Methodsmentioning

confidence: 99%

Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms

et al. 2010

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PDZ domains most commonly bind the C-terminus of their protein targets. Typically the C-terminal four residues of the protein target are considered as the binding motif, particularly the C-terminal residue (P0) and third-last residue (P-2) that form the major contacts with the PDZ domain's ''binding groove''. We solved crystal structures of seven human PDZ domains, including five of the seven PDLIM family members. The structures of GRASP, PDLIM2, PDLIM5, and PDLIM7 show a binding mode with only the C-terminal P0 residue bound in the binding groove. Importantly, in some cases, the P-2 residue formed interactions outside of the binding groove, providing insight into the influence of residues remote from the binding groove on selectivity. In the GRASP structure, we observed both canonical and noncanonical binding in the two molecules present in the asymmetric unit making a direct comparison of these binding modes possible. In addition, structures of the PDZ domains from PDLIM1 and PDLIM4 also presented here allow comparison with canonical binding for the PDLIM PDZ domain family. Although influenced by crystal packing arrangements, the structures nevertheless show that changes in the positions of PDZ domain side-chains and the aB helix allow noncanonical binding interactions.

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Section: Methodsmentioning

confidence: 99%

Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms

et al. 2010

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“…CAR2.V1_nohis was determined by using CAR2 as model. Refinement was done using programs PHENIX-Refine [45], REFMAC5 [46] and COOT [47]. Water molecules were added to well-defined difference electron density peaks at H-bond distance from the protein.…”

Section: Crystallization and Structure Determinationmentioning

confidence: 99%

Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition

Reichen

Hansen

Forzani

et al. 2016

Journal of Molecular Biology

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Armadillo repeat proteins (ArmRP) recognize their target peptide in extended conformation and bind, in a first approximation, two residues per repeat. They may thus form the basis for building a modular system, in which each repeat is complementary to a piece of the target peptide. Accordingly, preselected repeats could be assembled into specific binding proteins on demand and thereby avoid the traditional generation of every new binding molecule by an independent selection from a library.Stacked armadillo repeats, each consisting of 42 amino acids arranged in three α-helices, build an elongated superhelical structure. Here, we analyzed curvature variations in natural ArmRPs, and identified a repeat pair from yeast importin-α as having the optimal curvature geometry to be complementary to a peptide over its whole length. We employed a symmetric in silico design to obtain a uniform sequence for a stackable repeat while maintaining the desired curvature geometry.Computationally designed armadillo repeat proteins (dArmRPs) had to be stabilized by mutations to remove regions of higher flexibility, which were identified by molecular dynamics (MD) simulations in explicit solvent. Using an N-capping repeat from the consensus-design approach, two different crystal structures of dArmRP were determined. Although the experimental structures of dArmRP deviated from the designed curvature, the insertion of the most conserved binding pockets of natural ArmRPs onto the surface of dArmRPs resulted in binders against the expected peptide with low nanomolar affinities, similar to the binders from the consensus-design series.

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“…A solution of three heterodimeric complexes in the asymmetric unit was found (LLG = 6626). Following initial crystallographic refinement in REFMAC, 55 an initial F o -F c electron density map clearly revealed the bound ligands. Solvent structure was built using ARP/wARP, 56 and the ligands placed and the structure built using O.…”

Section: Structure Solution and Refinementmentioning

confidence: 99%

Structure of a GDP:AlF4 Complex of the SRP GTPases Ffh and FtsY, and Identification of a Peripheral Nucleotide Interaction Site

Focia

Gawronski-Salerno

Coon

et al. 2006

Journal of Molecular Biology

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The signal recognition particle (SRP) GTPases Ffh and FtsY play a central role in co-translational targeting of proteins, assembling in a GTP-dependent manner to generate the SRP targeting complex at the membrane. A suite of residues in FtsY have been identified that are essential for the hydrolysis of GTP that accompanies disengagement. We have argued previously on structural grounds that this region mediates interactions that serve to activate the complex for disengagement and term it the activation region. We report here the structure of a complex of the SRP GTPases formed in the presence of GDP:AlF 4 . This complex accommodates the putative transition-state analog without undergoing significant change from the structure of the ground-state complex formed in the presence of the GTP analog GMPPCP. However, small shifts that do occur within the shared catalytic chamber may be functionally important. Remarkably, an external nucleotide interaction site was identified at the activation region, revealed by an unexpected contaminating GMP molecule bound adjacent to the catalytic chamber. This site exhibits conserved sequence and structural features that suggest a direct interaction with RNA plays a role in regulating the activity of the SRP targeting complex.

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Efficient anisotropic refinement of macromolecular structures using FFT

Cited by 1,022 publications

References 18 publications

Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms

Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms

Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition

Structure of a GDP:AlF4 Complex of the SRP GTPases Ffh and FtsY, and Identification of a Peripheral Nucleotide Interaction Site

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