Biomedical subjects

Weiying Lin

Publications and source records attributed to Weiying Lin.

6 recordsLinked to original sources

PubMed2005

Site-specific labeling of cell surface proteins with biophysical probes using biotin ligase.

We report a highly specific, robust and rapid new method for labeling cell surface proteins with biophysical probes. The method uses the Escherichia coli enzyme biotin ligase (BirA), which sequence-specifically ligates biotin to a 15-amino-acid acceptor peptide (AP). We report that BirA also accepts a ketone isostere of biotin as a cofactor, ligating this probe to the AP with similar kinetics and retaining the high substrate specificity of the native reaction. Because ketones are absent from native cell surfaces, AP-fused recombinant cell surface proteins can be tagged with the ketone probe and then specifically conjugated to hydrazide- or hydroxylamine-functionalized molecules. We demonstrate this two-stage protein labeling methodology on purified protein, in the context of mammalian cell lysate, and on epidermal growth factor receptor (EGFR) expressed on the surface of live HeLa cells. Both fluorescein and a benzophenone photoaffinity probe are incorporated, with total labeling times as short as 20 min.

Biotinylation↗

PubMed2003

Conformational properties of nucleotide-based template-competitive HIV-1 reverse transcriptase inhibitors: analysis of enzyme binding modes.

Nucleotides 2-(4-azidophenacyl)thio-1,N6-etheno-2'-deoxyadenosine 5'-triphosphate 1 and its tetrafluoro analog 2 inhibit HIV-1 reverse transcriptase (RT) competitively relative to template. These template-competitive RT inhibitors (TCRTIs) were analyzed for conformational properties by molecular modeling and NMR analysis. Both inhibitors prefer sugar conformations of C2'-endo/C3'-exo with a high-anti glycosidic bond rotation and +sc/ap phosphate conformation (gamma). The major effect of the etheno group is to favor an extended, fully staggered anti conformation in the N1-C2-S-CH2 psi1 side chain rotation, and NMR analysis detects a long range sugar H4' to side chain phenyl meta-H NOE, a result consistent with this compact structure as an important contributor to the solution structure. The binding model generated places the phenyl side chain in a lipophilic pocket in the template grip region of the RT polymerase domain with the Mg-triphosphate complexed to active site carboxylates. The structures of the TCRTIs are compared with that of the template-competitive DNA polymerase inhibitor 2-(4-azidophenacyl)thio-2'-deoxyadenosine 5'-triphosphate 3, and a theoretical model for selectivity is proposed.

Binding, Competitive↗

PubMed2002

A strategy for the construction of caged diols using a photolabile protecting group.

Caged analogues of biologically active compounds have received widespread attention as temporally and spatially controlled probes of cell-based processes. Recently, a coumarin-4-ylmethyl derivative has been used to cage carboxylates, sulfonates, carbamates, and phosphates. We describe herein a synthetic strategy that furnishes photosensitive caged diols and provides an entry into the protection/photodeprotection of functionality with modest leaving group abilities.

Aldehydes↗

PubMed2002

Template-competitive inhibitors of HIV-1 reverse transcriptase: design, synthesis and inhibitory activity.

We report the design, synthesis and activity studies on a novel class of template-competitive reverse transcriptase inhibitors (TCRTIs). The TCRTIs are 1,N(6)-etheno analogues of a series of dATP-based template-competitive DNA polymerase inhibitors synthesized in our laboratory (Moore, B. M.; Jalluri, R.; Doughty, M.B. Biochemistry 1996, 35, 11634). Thus, nucleotides 2-(4-azidophenacyl)thio-1,N(6)-etheno-2'-deoxyadenosine 5'-triphosphate 1, the tetrafluoro analogue 2-(4-azido-2,3,5,6-tetrafluorophenacyl)thio-1,N(6)-etheno-2'-deoxyadenosine 5'-triphosphate 2 and its analogues were synthesized by alkylation of 2-thio-1,N(6)-etheno-2'-deoxyadenosine 5'-monophosphate with the corresponding chloro- or bromo-alkyl halides and converted to the triphosphate. Kinetically, nucleotides 1 and 2 are both competitive inhibitors of reverse transcriptase versus template/primer with K(i)'s of 8.0 and 7.4 microM, respectively, and non-competitive inhibitors versus TTP with K(i)'s of 15 and 10 microM, respectively. Nucleotide 3, which differs from 1 only in that it lacks the etheno group, non-complementary nucleotide triphosphates, and related monophosphates and nucleosides, are completely inactive as inhibitors of reverse transcriptase at concentrations up to 1 mM. Photoinactivation of RT by 1 was both time- and concentration-dependent, and protected by template/primer but not by dNTPs. The concentration-dependent inactivation data gave a K(D,app) of 17.2 microM and maximum inactivation of 90%, and radiolabeled [beta, gamma-32P]-1 photoincorporated specifically and covalently into the p66 subunit of RT. Thus the photoinactivation data support our main conclusion from the kinetic data that this class of RT inhibitors are non-substrate and template-competitive.

Binding, Competitive↗

PubMed2002

Characterization of a binding site for template competitive inhibitors of HIV-1 reverse transcriptase using photolabeling derivatives.

Analogues of a novel class of template-competitive reverse transcriptase inhibitors (Li, K.; Lin, W.; Chong, K. H.; Moore, B. M.; Doughty, M. B. Bioorg. Med. Chem. 2002, 10, 507) were analyzed as photoprobes of HIV-1 reverse transcriptase (RT) heterodimer. The two photoprobes, 2-(4-azidophenacyl)thio-1,N(6)-etheno-2'-deoxyadenosine 5'-triphosphate 2 and the tetrafluoro analogue 2-(4-azido-2,3,5,6-tetrafluorophenacyl)thio-1,N(6)-etheno-2'-deoxyadenosine 5'-triphosphate 3, photodecomposed at 3500 A with half-lives of 4.0 and 2.5 min, respectively. Analysis of the photoproducts of 2m demonstrated that the etheno group is stable but the azido decomposes primarily to the 2-(S-[3H-diazepinon-4-yl]thio)-1,N(6)-etheno-dAMP. Photolysis of both 2 and 3 with RT resulted in a time-dependent loss of activity, with maximum inactivation of 83 and 60%, respectively. Both 2 and 3 showed concentration-dependent photoinactivation of RT in the concentration range from 0 to 100 microM, with EC(50)s of 20 and 25 microM and maximum inactivation of 80 and 60%, respectively. Both the time and concentration dependent photoinactivation were strongly protected by template-primer, but only poorly inhibited by even high concentrations of TTP. Radiolabeled analogues [beta,gamma-(32)P]-2 and [beta,gamma-(32)P]-3 photoincorporated into the p66 subunit, an incorporation also protected by template primer. Identification of the site of incorporation was problematic for both photoprobes, but evidence presented is consistent with labeling sites for the phenacyl side chains of both 2 and 3 in the template grip. Nevertheless, the photoinactivation and incorporation data are consistent with our earlier conclusions from the kinetic data that these inhibitors are specific for the free form of RT in competition with template/primer, and thus represent a novel class of inhibitors.

Adenosine Triphosphate↗

PubMed2002

Spatially discrete, light-driven protein expression.

Transgene-based inducible expression systems offer the potential to study the influence of any gene at any point during an organism's lifetime. However, the expression of individual genes is both temporally and spatially (i.e., cell/tissue)-regulated. The inducible gene expression systems devised to date do not offer fine spatial control over gene expression. We describe herein the creation and study of a light-activatable, ecdysone-inducible gene expression system. We have constructed the first example of a caged ecdysteroid, which is virtually inactive as an inducing agent in a luciferase-based gene expression system. However, upon exposure to brief illumination, the caged ecdysteroid is rapidly converted into active beta-ecdysone. Caged beta-ecdysone is cell permeable, can be intracellularly photouncaged, and, in combination with spot illumination, can be used to drive spatially discrete protein expression in a multicellular setting.

Animals↗