Publications by authors named "Ayat Yaseen"

6 Publications

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Structure of the FA core ubiquitin ligase closing the ID clamp on DNA.

Nat Struct Mol Biol 2021 03 8;28(3):300-309. Epub 2021 Mar 8.

Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

The Fanconi anemia (FA) pathway is essential for the repair of DNA interstrand crosslinks. Central to the pathway is the FA core complex, a ubiquitin ligase of nine subunits that monoubiquitinates the FANCI-FANCD2 (ID) DNA clamp. The 3.1 Å structure of the 1.1-MDa human FA core complex, described here, reveals an asymmetric assembly with two copies of all but the FANCC, FANCE and FANCF subunits. The asymmetry is crucial, as it prevents the binding of a second FANCC-FANCE-FANCF subcomplex that inhibits the recruitment of the UBE2T ubiquitin conjugating enzyme, and instead creates an ID binding site. A single active site then ubiquitinates FANCD2 and FANCI sequentially. We also present the 4.2-Å structures of the human core-UBE2T-ID-DNA complex in three conformations captured during monoubiquitination. They reveal the core-UBE2T complex remodeling the ID-DNA complex, closing the clamp on the DNA before ubiquitination. Monoubiquitination then prevents clamp opening after release from the core.
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http://dx.doi.org/10.1038/s41594-021-00568-8DOI Listing
March 2021

Crystal structures of the synthetic inter-mediate 3-[(6-chloro-7-purin-7-yl)meth-yl]cyclo-butan-1-one, and of two oxetanocin derivatives: 3-[(6-chloro-8,9-di-hydro-7-purin-7-yl)meth-yl]cyclo-butan-1-ol and 3-[(6-chloro-9-purin-9-yl)meth-yl]cyclo-butan-1-ol.

Acta Crystallogr E Crystallogr Commun 2019 Jun 3;75(Pt 6):732-737. Epub 2019 May 3.

Department of Chemistry, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada.

The crystal structures of an inter-mediate, CHClNO, 3-[(6-chloro-7-purin-7-yl)meth-yl]cyclo-butan-1-one (I), and two N-7 and N-9 regioisomeric oxetanocin nucleoside analogs, CHClNO, 3-[(6-chloro-8,9-di-hydro-7-purin-7-yl)meth-yl]cyclo-butan-1-ol (II) and CHClNO, 3-[(6-chloro-9-purin-9-yl)meth-yl]cyclo-butan-1-ol (IV), are reported. The crystal structures of the nucleoside analogs confirmed the reduction of the N-7- and N-9-substituted cyclo-butano-nes with LiAl(OtBu) to occur with facial selectivity, yielding -nucleosides analogs similar to those found in nature. Reduction of the purine ring of the N-7 cyclo-butanone to a di-hydro-purine was observed for compound (II) but not for the purine ring of the N-9 cyclo-butanone on formation of compound (IV). In the crystal of (I), mol-ecules are linked by a weak Cl⋯O inter-action, forming a 2 helix along [010]. The helices are linked by offset π-π inter-actions [inter-centroid distance = 3.498 (1) Å], forming layers parallel to (101). In the crystal of (II), mol-ecules are linked by pairs of O-H⋯N hydrogen bonds, forming inversion dimers with an (8) ring motif. The dimers are linked by O-H⋯N hydrogen bonds, forming chains along [001], which in turn are linked by C-H⋯π and offset π-π inter-actions [inter-centroid distance = 3.509 (1) Å], forming slabs parallel to the plane. In the crystal of (IV), mol-ecules are linked by O-H⋯N hydrogen bonds, forming chains along [101]. The chains are linked by C-H⋯N and C-H⋯O hydrogen bonds and C-H⋯π and offset π-π inter-actions [inter-centroid distance = 3.364 (1) Å], forming a supra-molecular framework.
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http://dx.doi.org/10.1107/S2056989019004432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6658957PMC
June 2019

Protein Nanotubes: From Bionanotech towards Medical Applications.

Biomedicines 2019 Jun 23;7(2). Epub 2019 Jun 23.

Patent Law Department, Bawa Biotech LLC, Ashburn, VA 20147, USA.

Nanobiotechnology involves the study of structures found in nature to construct nanodevices for biological and medical applications with the ultimate goal of commercialization. Within a cell most biochemical processes are driven by proteins and associated macromolecular complexes. Evolution has optimized these protein-based nanosystems within living organisms over millions of years. Among these are flagellin and pilin-based systems from bacteria, viral-based capsids, and eukaryotic microtubules and amyloids. While carbon nanotubes (CNTs), and protein/peptide-CNT composites, remain one of the most researched nanosystems due to their electrical and mechanical properties, there are many concerns regarding CNT toxicity and biodegradability. Therefore, proteins have emerged as useful biotemplates for nanomaterials due to their assembly under physiologically relevant conditions and ease of manipulation via protein engineering. This review aims to highlight some of the current research employing protein nanotubes (PNTs) for the development of molecular imaging biosensors, conducting wires for microelectronics, fuel cells, and drug delivery systems. The translational potential of PNTs is highlighted.
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http://dx.doi.org/10.3390/biomedicines7020046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6630890PMC
June 2019

Synthesis of cyclobutane nucleoside analogues 3: Preparation of carbocyclic derivatives of oxetanocin.

Nucleosides Nucleotides Nucleic Acids 2018 6;37(9):518-531. Epub 2018 Sep 6.

a Department of Chemistry , York University , Toronto , Ontario , Canada.

A synthesis of cyclobutene nucleoside analogs in which the nucleobase is tethered by a methylene group is described. The coupling of 6-chloropurine with 3-hydroxymethyl-cyclobutanone proceeds via its triflate to give both N-7 and N-9 regioisomers with relative yields corresponding to the calculated charge distribution of the 6-chloropurinyl anion. The stereoselective reduction of the N-alkylated ketones yielded quantitatively one stereoisomer in each case. The structural assignments were based on spectroscopic data and single crystal X-ray diffraction. Attempts to photoexcite the N-7 and N-9 ketones in order to promote ring-expansion did not ensue. Preliminary evidence suggests a photodecarbonylation to cyclopropanes took place.
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http://dx.doi.org/10.1080/15257770.2018.1500697DOI Listing
July 2019

Structural flexibility in the Helicobacter pylori peptidyl-prolyl cis,trans-isomerase HP0175 is achieved through an extension of the chaperone helices.

J Struct Biol 2018 11 1;204(2):261-269. Epub 2018 Sep 1.

Department of Chemistry, York University, Toronto M3J 1P3, Canada; Centre for Research of Biomolecular Interactions, York University, Toronto M3J 1P3, Canada. Electronic address:

Helicobacter pylori infects the gastric epithelium of half the global population, where infections can persist into adenocarcinomas and peptic ulcers. H. pylori secretes several proteins that lend to its pathogenesis and survival including VacA, CagA, γ-glutamyltransferase and HP0175. HP0175, also known as HpCBF2, classified as a peptidyl-prolyl cis,trans-isomerase, has been shown to induce apoptosis through a cascade of mechanisms initiated though its interaction with toll like receptor 4 (TLR4). Here, we report the structure of apo-HP0175 at 2.09 Å with a single monomer in the asymmetric unit. Chromatographic, light scattering and mass spectrometric analysis of HP0175 in solution indicate that the protein is mainly monomeric under low salt conditions, while increasing ionic interactions facilitates protein dimerization. A comparison of the apo-HP0175 structure to that of the indole-2-carboxylic acid-bound form shows movement of the N- and C-terminal helices upon interaction of the catalytic residues in the binding pocket. Helix extension of the N/C chaperone domains between apo and I2CA-bound HP0175 supports previous findings in parvulin PPIases for their role in protein stabilization (and accommodation of variable protein lengths) of those undergoing catalysis.
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http://dx.doi.org/10.1016/j.jsb.2018.08.017DOI Listing
November 2018

Conjugative Mating Assays for Sequence-specific Analysis of Transfer Proteins Involved in Bacterial Conjugation.

J Vis Exp 2017 01 4(119). Epub 2017 Jan 4.

Department of Chemistry, York University; The Centre for Research on Biomolecular Interactions, York University;

The transfer of genetic material by bacterial conjugation is a process that takes place via complexes formed by specific transfer proteins. In Escherichia coli, these transfer proteins make up a DNA transfer machinery known as the mating pair formation, or DNA transfer complex, which facilitates conjugative plasmid transfer. The objective of this paper is to provide a method that can be used to determine the role of a specific transfer protein that is involved in conjugation using a series of deletions and/or point mutations in combination with mating assays. The target gene is knocked out on the conjugative plasmid and is then provided in trans through the use of a small recovery plasmid harboring the target gene. Mutations affecting the target gene on the recovery plasmid can reveal information about functional aspects of the target protein that result in the alteration of mating efficiency of donor cells harboring the mutated gene. Alterations in mating efficiency provide insight into the role and importance of the particular transfer protein, or a region therein, in facilitating conjugative DNA transfer. Coupling this mating assay with detailed three-dimensional structural studies will provide a comprehensive understanding of the function of the conjugative transfer protein as well as provide a means for identifying and characterizing regions of protein-protein interaction.
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http://dx.doi.org/10.3791/54854DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5351875PMC
January 2017