Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.The workshop was supported by funding to RCSB PDB by the National Science Foundation (DBI 1338415); PDBe by the Wellcome Trust (104948); PDBj by JST-NBDC; BMRB by the National Institute of General Medical Sciences (GM109046); D3R by the National Institute of General Medical Sciences (GM111528); registration fees from industrial participants; and tax-deductible donations to the wwPDB Foundation by the Genentech Foundation and the Bristol-Myers Squibb Foundation.This is the final version of the article. It first appeared from Cell Press via https://doi.org//10.1016/j.str.2016.02.01

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30–31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.This is the publisher’s final pdf. The published article is copyrighted by Elsevier (Cell Press) and can be found at: http://www.cell.com/structure/hom

Crystal structure of a light-harvesting protein C-phycocyanin from Spirulina platensis

The crystal structure of C-phycocyanin, a light-harvesting phycobiliprotein from cyanobacteria (blue-green algae) Spirulina platensis has been solved by molecular replacement technique. The crystals belong to space group P21 with cell parameters a = 107.20, b = 115.40, c = 183.04 Å; β = 90.2°. The structure has been refined to a crystallographic R factor of 19.2% (Rfree = 23.9%) using the X-ray diffraction data extending up to 2.2 Å resolution. The asymmetric unit of the crystal cell consists of two (αβ)6-hexamers, each hexamer being the functional unit in the native antenna rod of cyanobacteria. The molecular structure resembles that of other reported C-phycocyanins. However, the unique form of aggregation of two (αβ)6-hexamers in the crystal asymmetric unit, suggests additional pathways of energy transfer in lateral direction between the adjacent hexamers involving β155 phycocyanobilin chromophores

Role of a two-residue spacer in an α,β-didehydrophenylalanine containing hexapeptide: crystal and solution structure of Boc-Val-ΔPhe-Leu-Ala-ΔPhe-Ala-OMe

The peptide Boc-Val<SUP>1</SUP>-&#916;Phe<SUP>2</SUP>-Leu<SUP>3</SUP>-Ala<SUP>4</SUP>-&#916;Phe<SUP>5</SUP>-Ala<SUP>6</SUP>-OMe has been examined for the structural consequence of placing a two-residue segment between the &#916;Phe residues. The peptide is stabilized by four consecutive &#946;-turns. The overall conformation of the molecule is a right-handed 3<SUB>10</SUB>-helix, with average (&#934;, &#968;) values (&#8722;67.7&#176;, &#8722;22.7&#176;), unwound at the C-terminus. The <SUP>1</SUP>H NMR results also suggest that the peptide maintains its 3<SUB>10</SUB>-helical structure in solution as observed in the crystal state. The crystal structure is stabilized through head-to-tail hydrogen bonds and a repertoire of aromatic interactions laterally directed between adjacent helices, which are antiparallel to each other. The aromatic ring of &#916;Phe<SUP>5</SUP> forms the hub of multicentred interactions, namely as a donor in aromatic C-H<SUP>...</SUP>&#960; and aromatic C-H<SUP>...</SUP>O-C interactions and as an acceptor in a CH<SUB>3</SUB><SUP>...</SUP>&#960; interaction. The present structure uniquely illustrates the unusual capability of a &#916;Phe ring to host such concerted interactions and suggests its exploitation in introducing long-range interactions in the folding of supersecondary structures

Crystal Structure of a Light-Harvesting Protein C-Phycocyanin from Spirulina platensis

The crystal structure of C-phycocyanin, a light-harvesting phycobiliprotein from cyanobacteria (blue-green algae) Spirulina platensis has been solved by molecular replacement technique. The crystals belong to space group $P2_1$ with cell parameters a = 107.20, b = 115.40, c = 183.04 \AA; $\beta=90.2^o$. The structure has been refined to a crystallographic R factor of 19.2% $(R_{free}=23.9$%) using the X-ray diffraction data extending up to 2.2 \AA resolution. The asymmetric unit of the crystal cell consists of two $(\alpha \beta)_6$-hexamers, each hexamer being the functional unit in the native antenna rod of cyanobacteria. The molecular structure resembles that of other reported C-phycocyanins. However, the unique form of aggregation of two $(\alpha \beta)_6$-hexamers in the crystal asymmetric unit, suggests additional pathways of energy transfer in lateral direction between the adjacent hexamers involving $\beta 155$ phycocyanobilin chromophores

High-throughput mutagenesis reveals unique structural features of human ADAR1

Human ADAR proteins are responsible for RNA editing, conversion of adenosine to inosine in double-stranded RNA. Here the authors report a previously unknown zinc ion-binding site in the catalytic domain of human ADAR1 using high throughput mutagenesis, biochemical assay and Rosetta-based protein structure modeling

High-throughput mutagenesis reveals unique structural features of human ADAR1.

Adenosine Deaminases that act on RNA (ADARs) are enzymes that catalyze adenosine to inosine conversion in dsRNA, a common form of RNA editing. Mutations in the human ADAR1 gene are known to cause disease and recent studies have identified ADAR1 as a potential therapeutic target for a subset of cancers. However, efforts to define the mechanistic effects for disease associated ADAR1 mutations and the rational design of ADAR1 inhibitors are limited by a lack of structural information. Here, we describe the combination of high throughput mutagenesis screening studies, biochemical characterization and Rosetta-based structure modeling to identify unique features of ADAR1. Importantly, these studies reveal a previously unknown zinc-binding site on the surface of the ADAR1 deaminase domain which is important for ADAR1 editing activity. Furthermore, we present structural models that explain known properties of this enzyme and make predictions about the role of specific residues in a surface loop unique to ADAR1

High-throughput mutagenesis reveals unique structural features of human ADAR1.

Adenosine Deaminases that act on RNA (ADARs) are enzymes that catalyze adenosine to inosine conversion in dsRNA, a common form of RNA editing. Mutations in the human ADAR1 gene are known to cause disease and recent studies have identified ADAR1 as a potential therapeutic target for a subset of cancers. However, efforts to define the mechanistic effects for disease associated ADAR1 mutations and the rational design of ADAR1 inhibitors are limited by a lack of structural information. Here, we describe the combination of high throughput mutagenesis screening studies, biochemical characterization and Rosetta-based structure modeling to identify unique features of ADAR1. Importantly, these studies reveal a previously unknown zinc-binding site on the surface of the ADAR1 deaminase domain which is important for ADAR1 editing activity. Furthermore, we present structural models that explain known properties of this enzyme and make predictions about the role of specific residues in a surface loop unique to ADAR1