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Preview: Forthcoming article in Acta Crystallographica Section D: Biological Crystallography

Forthcoming article in Acta Crystallographica Section D Structural Biology



Acta Crystallographica Section D: Structural Biology welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports o



 



Structural analysis of the bright monomeric yellow-green fluorescent protein mNeonGreen obtained by directed evolution
The structures of the fluorescent proteins lanYFP and mNeonGreen from B. lanceolatum are described, providing a structural understanding of the directed evolution process from lanYFP to mNeonGreen. A specific radiation-damage study has been performed for mNeonGreen.






Polder maps: improving OMIT maps by excluding bulk solvent
Residual OMIT maps can be improved by selective exclusion of the bulk-solvent from the OMIT region.



Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core
A crystal structure of the U6 snRNP core from yeast shows that mutation of the U6 internal stem-loop (ISL) does not alter the overall topology of the snRNP, but suggests structural plasticity in the ISL.



The ER stress sensor PERK luminal domain functions as a molecular chaperone to interact with misfolded proteins
The PERK luminal domain can function as a molecular chaperone to recognize and bind misfolded proteins. The crystal structure of the PERK luminal domain suggests that it may utilize a flexible β-sandwich domain to recognize and interact with a broad range of misfolded proteins.



Molecular determinants of substrate specificity revealed by the structure of Clostridium thermocellum arabinofuranosidase 43A from glycosyl hydrolase family 43 subfamily 16
The structure of C. thermocellum arabinofuranosidase 43A reveals how the enzyme acts specifically in the removal of arabinose side chains from arabinoxylan but not from pectic arabinan.



The N14 anti-afamin antibody Fab: a rare VL1 CDR glycosylation, crystallographic re-sequencing, molecular plasticity and conservative versus enthusiastic modelling
Models of the VL1 glycosylated Fab fragment independently refined from two non-apparent (pseudo) isomorphous crystals show significant differences, allowing the meaning of accuracy in structure description to be revisited, while at the same time inviting reflections about the benefits and boundaries of complex solvent modelling and validation.



Improved radiation dose efficiency in solution SAXS using a sheath flow sample environment
Coflow is a new method for delivering radiation-sensitive biological and other solution-based samples to high-brightness X-ray beamlines that exploits laminar flow to ameliorate radiation-damage limitations and provides a host of practical improvements associated with these types of experiments.



Strategies for carbohydrate model building, refinement and validation
This article addresses many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and electron cryo-microscopy are expected to overlap in the next decade.



Molecular symmetry-constrained systematic search approach to structure solution of the coiled-coil SRGAP2 F-BARx domain
The F-BARx domain of SRGAP2 was produced for crystallization by co-expressing it with the carboxy domains of the protein. The F-BARx crystal structure was determined by a molecular symmetry-constrained systematic search, utilizing the conserved biological symmetry of the F-BAR fold, an approach that is shown to be useful in solving other F-BAR structures.



Combining X-ray and neutron crystallography with spectroscopy
The use of neutron crystallography and in situ spectroscopy to study enzyme mechanism is discussed.



Twilight reloaded: the peptide experience
The potential causes of severe misinterpretation of peptide density in a significant number of protein–peptide complex structures are analyzed, together with suggestions for good practice and specific education aimed to minimize overinterpretation and mistakes in protein–peptide complex structure models.



On the interpretation of reflectivity data from lipid bilayers in terms of molecular-dynamics models
A method is presented for producing continuous scattering length density profiles from simulated molecular-dynamics structures of biomembranes for the analysis of reflectometry data from lipid layers.



Using more than 801 296 small-molecule crystal structures to aid in protein structure refinement and analysis
A guide to how the Cambridge Structural Database can be used to aid macromolecular crystallography.



Glycoblocks: a schematic three-dimensional representation for glycans and their interactions
With structural glycoscience finally gaining popularity, the need for a clear way of depicting glycans and their interactions in three dimensions is more pressing than ever. Here the Glycoblocks representation is introduced, which combines a simplified bonding-network depiction with the familiar two-dimensional glycan notation brought into three-dimensions.