Garry W. Buchko

Constraint of DNA on Functionalized Graphene Improves its Biostability and Specificity

The single-stranded DNA constrained on graphene surface is effectively protected from enzymatic cleavage by DNase I. The anisotropy, fluorescence, NMR, and CD studies suggest that the single-stranded DNA is promptly adsorbed onto graphene forming strong molecular interactions. Furthermore, the constraint of DNA probe on graphene improves the specificity of its response to complementary DNA. These findings will promote the further application of graphene in biotechnology and biomedical fields.

Accurate de novo design of hyperstable constrained peptides.

Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks generally have shapes that have evolved to fit precisely into binding pockets on their targets. Such peptides can have excellent pharmaceutical properties, combining the stability and tissue penetration of small-molecule drugs with the specificity of much larger protein therapeutics. The ability to design constrained peptides with precisely specified tertiary structures would enable the design of shape-complementary inhibitors of arbitrary targets. Here we describe the development of computational methods for accurate de novo design of conformationally restricted peptides, and the use of these methods to design 18–47 residue, disulfide-crosslinked peptides, a subset of which are heterochiral and/or N–C backbone-cyclized. Both genetically encodable and non-canonical peptides are exceptionally stable to thermal and chemical denaturation, and 12 experimentally determined X-ray and NMR structures are nearly identical to the computational design models. The computational design methods and stable scaffolds presented here provide the basis for development of a new generation of peptide-based drugs.

1 H, 13C and 15N nuclear magnetic resonance analysis and chemical features of the two main radical oxidation products of 2′-deoxyguanosine: oxazolone and imidazolone nucleosides

The two primary one-electron oxidation and ˙OH-mediated decomposition products of 2′-deoxyguanosine 1 are 2,2-diamino-4-[(2-deoxy-β-D-erythro-pentofuranosyl)amino]-2,5-dihydrooxazol-5-one 3 (dZ) and its precursor, 2-amino-5-[(2-deoxy-β-D-erythro-pentofuranosyl)amino]-4H-imidazol-4-one 2 (dIz). Here, we describe in detail the spectroscopic and chemical properties of both oxidative DNA lesions. The structures for dZ 3 and dIz 2 were determined by fast-atom bombardment mass spectrometry, UV spectroscopy, IR spectroscopy, together with 1H, 13C, 15N and 17O 1D and 2D NMR spectroscopy. In neutral aqueous solution dIz 2 is hydrolysed to dZ 3 (t½= 147 min at 37 °C) with the incorporation of one molecule of water. Hot alkali treatment (65 °C; pH 13) of dIz 2 and dZ 3 quantitatively results in the release of guanidine (t½= 3.3 and 3.1 min, respectively). The latter property allowed us to develop a specific and sensitive method for the detection of the two modified nucleosides 2 and 3. Methoxyamine reacts quantitatively with 3′,5′-di-O-acetyl-dIz 2a 120-times faster than with 3′,5′-di-O-acetyl-dZ 3a to form four 3,5-di-O-acetyl-2-deoxy-D-erythro-pentose–methoxyamine isomers.

The Seattle Structural Genomics Center for Infectious Disease (SSGCID)

The NIAID-funded Seattle Structural Genomics Center for Infectious Disease (SSGCID) is a consortium established to apply structural genomics approaches to potential drug targets from NIAID priority organisms for biodefense and emerging and re-emerging diseases. The mission of the SSGCID is to determine approximately 400 protein structures over the next five years. In order to maximize biomedical impact, ligand-based drug-lead discovery campaigns will be pursued for a small number of high-impact targets. Here we review the centers target selection processes, which include pro-active engagement of the infectious disease research and drug therapy communities to identify drug targets, essential enzymes, virulence factors and vaccine candidates of biomedical relevance to combat infectious diseases. This is followed by a brief overview of the SSGCID structure determination pipeline and ligand screening methodology. Finally, specifics of our resources available to the scientific community are presented. Physical materials and data produced by SSGCID will be made available to the scientific community, with the aim that they will provide essential groundwork benefiting future research and drug discovery.

Combining functional and structural genomics to sample the essential Burkholderia structome.

Background The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite. Methodology/Principal Findings We experimentally identified 406 putative essential genes in B. thailandensis, a low-virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq). We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID) structure determination pipeline. To maximize structural coverage of these targets, we applied an “ortholog rescue” strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs) from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail. Conclusions/Significance This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against infections and diseases caused by Burkholderia. All expression clones and proteins created in this study are freely available by request.

Structural and Functional Studies of a Phosphatidic Acid-Binding Antifungal Plant Defensin MtDef4: Identification of an RGFRRR Motif Governing Fungal Cell Entry

MtDef4 is a 47-amino acid cysteine-rich evolutionary conserved defensin from a model legume Medicago truncatula. It is an apoplast-localized plant defense protein that inhibits the growth of the ascomycetous fungal pathogen Fusarium graminearum in vitro at micromolar concentrations. Little is known about the mechanisms by which MtDef4 mediates its antifungal activity. In this study, we show that MtDef4 rapidly permeabilizes fungal plasma membrane and is internalized by the fungal cells where it accumulates in the cytoplasm. Furthermore, analysis of the structure of MtDef4 reveals the presence of a positively charged γ-core motif composed of β2 and β3 strands connected by a positively charged RGFRRR loop. Replacement of the RGFRRR sequence with AAAARR or RGFRAA abolishes the ability of MtDef4 to enter fungal cells, suggesting that the RGFRRR loop is a translocation signal required for the internalization of the protein. MtDef4 binds to phosphatidic acid (PA), a precursor for the biosynthesis of membrane phospholipids and a signaling lipid known to recruit cytosolic proteins to membranes. Amino acid substitutions in the RGFRRR sequence which abolish the ability of MtDef4 to enter fungal cells also impair its ability to bind PA. These findings suggest that MtDef4 is a novel antifungal plant defensin capable of entering into fungal cells and affecting intracellular targets and that these processes are mediated by the highly conserved cationic RGFRRR loop via its interaction with PA.

Structural genomics of infectious disease drug targets: the SSGCID

An introduction and overview of the focus, goals and overall mission of the Seattle Structural Genomics Center for Infectious Disease (SSGCID) is given.

Characterization of two potentially universal turn motifs that shape the repeated five-residues fold—Crystal structure of a lumenal pentapeptide repeat protein from Cyanothece 51142

The genome of the diurnal cyanobacterium Cyanothece sp. PCC 51142 has recently been sequenced and observed to contain 35 pentapeptide repeat proteins (PRPs). These proteins, while present throughout the prokaryotic and eukaryotic kingdoms, are most abundant in cyanobacteria. The sheer number of PRPs in cyanobacteria coupled with their predicted location in every cellular compartment argues for important, yet unknown, physiological and biochemical functions. To gain biochemical insights, the crystal structure for Rfr32, a 167‐residue PRP with an N‐terminal 29‐residue signal peptide, was determined at 2.1 Å resolution. The structure is dominated by 21 tandem pentapeptide repeats that fold into a right‐handed quadrilateral β‐helix, or Rfr‐fold, as observed for the tandem pentapeptide repeats in the only other PRP structure, the mycobacterial fluoroquinoline resistance protein MfpA from Mycobacterium tuberculosis. Sitting on top of the Rfr‐fold are two short, antiparallel α‐helices, bridged with a disulfide bond, that perhaps prevent edge‐to‐edge aggregation at the C terminus. Analysis of the main‐chain (Φ,Ψ) dihedral orientations for the pentapeptide repeats in Rfr32 and MfpA makes it possible to recognize the structural details for the two distinct types of four‐residue turns adopted by the pentapeptide repeats in the Rfr‐fold. These turns, labeled type II and type IV β‐turns, may be universal motifs that shape the Rfr‐fold in all PRPs.

A Bayesian integration model of high-throughput proteomics and metabolomics data for improved early detection of microbial infections.

High-throughput (HTP) technologies offer the capability to evaluate the genome, proteome, and metabolome of an organism at a global scale. This opens up new opportunities to define complex signatures of disease that involve signals from multiple types of biomolecules. However, integrating these data types is difficult due to the heterogeneity of the data. We present a Bayesian approach to integration that uses posterior probabilities to assign class memberships to samples using individual and multiple data sources; these probabilities are based on lower-level likelihood functions derived from standard statistical learning algorithms. We demonstrate this approach on microbial infections of mice, where the bronchial alveolar lavage fluid was analyzed by three HTP technologies, two proteomic and one metabolomic. We demonstrate that integration of the three datasets improves classification accuracy to approximately 89% from the best individual dataset at approximately 83%. In addition, we present a new visualization tool called Visual Integration for Bayesian Evaluation (VIBE) that allows the user to observe classification accuracies at the class level and evaluate classification accuracies on any subset of available data types based on the posterior probability models defined for the individual and integrated data.

Enzyme design from the bottom up: an active nickel electrocatalyst with a structured peptide outer coordination sphere.

Catalytic, peptide-containing metal complexes with a well-defined peptide structure have the potential to enhance molecular catalysts through an enzyme-like outer coordination sphere. Here, we report the synthesis and characterization of an active, peptide-based metal complex built upon the well-characterized hydrogen production catalyst [Ni(P(Ph)2N(Ph))2](2+) (P(Ph)2N(Ph)=1,3,6-triphenyl-1-aza-3,6-diphosphacycloheptane). The incorporated peptide maintains its β-hairpin structure when appended to the metal core, and the electrocatalytic activity of the peptide-based metal complex (≈100,000 s(-1)) is enhanced compared to the parent complex ([Ni(P(Ph)2N(APPA))2](2+); ≈50,500 s(-1)). The combination of an active molecular catalyst with a structured peptide provides a scaffold that permits the incorporation of features of an enzyme-like outer-coordination sphere necessary to create molecular electrocatalysts with enhanced functionality.