Biomedical subjects

Alanna Schepartz

Publications and source records attributed to Alanna Schepartz.

22 records · Page 2Linked to original sources

PubMed2003

Miniature homeodomains: high specificity without an N-terminal arm.

Recently, we described a strategy for the design of miniature proteins that bind DNA and protein surfaces with high affinity and selectivity. This strategy involves identifying the functional epitope required for macromolecular recognition by a natural protein and presenting it on a small, stable protein scaffold. In previous work, high-affinity DNA recognition was achieved only when the miniature protein contained the complete functional epitope. Here we report a miniature homeodomain that recognizes its 6-bp target site in the nanomolar concentration range at 25 degrees C, despite the absence of DNA contact residues located along the homeodomain N-terminal arm. We conclude that miniature proteins can achieve high affinity and selectivity for DNA by design even when the functional epitope is incomplete by using pre-organization to effectively compensate for lost protein-DNA contacts. In this case it has been possible to miniaturize both the recognition surface and the structural framework of a globular protein fold.

Amino Acid Sequence↗

PubMed2002

Gal4-VP16 and Gal4-AH increase the orientational and axial specificity of TATA box recognition by TATA box binding protein.

Previous work has shown that binding of the TATA box binding protein (TBP) to the TATA box is a rate-limiting step during pre-initiation complex (PIC) formation. Although the transcription of eukaryotic genes normally proceeds in one direction, studies in solution have shown that TBP lacks the information necessary to orient itself on the TATA box. Instead, yeast TBP binds TATA-containing promoters in two orientations that are related by a 180 rotation about TBP's pseudo-2-fold symmetry axis. Recruitment of PIC components by gene-specific activators is considered a primary mechanism of transcriptional enhancement. Here we ask whether activators might function, at least in part, by increasing the fraction of PICs assembled with TBP bound in the orientation necessary for transcription. We use DNA affinity cleavage and a TBP-phenanthroline-copper conjugate to monitor the orientation of TBP in the presence of the well-studied activators Gal4-VP16 and Gal4-AH. In the absence of a transcriptional activator, only 51% of the TBP x TATA box complexes were bound in the orientation necessary for the initiation of transcription. However, in the presence of saturating Gal4-VP16, 87% of the TBP bound to the TATA box was oriented correctly at equilibrium. This increase in orientational specificity corresponds to a free energy difference (Delta Delta G(obs)) of 1.1 kcal x mol(-1) and was accompanied by a dramatic increase in axial specificity, reminiscent of the effects of transcription factors TFIIB and TFIIA reported previously. Gal4-AH also enhanced the orientational and axial specificity of the TBP x TATA complex, although to a lesser extent. We suggest that these effects on specificity represent a variation of recruitment, since they require direct interactions between the activator and a PIC component but only increase the effective concentration of the correctly oriented PIC component. These findings add to increasing evidence that recruitment may encompass a broad range of mechanisms.

Binding Sites↗

PubMed2002

A view to a kill: ligands for Bcl-2 family proteins.

Apoptosis is the essential process of programmed cell death that, in multicellular organisms, regulates development and maintains homeostasis. Defects in the apoptotic molecular machinery that result in either excessive or insufficient apoptosis are observed in a remarkably wide range of human disease, prompting intense interest in pro- and anti-apoptotic proteins as therapeutic targets. A number of recent reports have described the discovery of ligands for anti-apoptotic Bcl-2 family proteins by a variety of approaches, including computational, combinatorial and evolutionary strategies. Both the design of ligands and the exploration of their mechanisms of action have been greatly enhanced by recent high-resolution structure determinations of proteins from this family. Several of the newly discovered ligands promote apoptosis, and some do so even in the face of overexpressed anti-apoptotic Bcl-2 proteins. Ligands that overcome the protective effects associated with up-regulation of anti-apoptotic Bcl-2 proteins represent especially promising therapeutic leads.

Apoptosis↗

PubMed2001

Design and Evolution of a Miniature Bcl-2 Binding Protein We thank the HHMI Biopolymer/Keck Foundation Biotechnology Resource Laboratory (Yale University School of Medicine, New Haven, CT) for oligonucleotide and peptide synthesis and amino acid analysis and Professor Jennifer Doudna (Yale University) for use of a Perseptive Voyager-DE (MALDI-TOF) mass spectrometer. We are grateful also to Dr. Junying Yuan and Dr. Alexi Degterev (Harvard Medical School) for a generous gift of Bcl-X(L)-His(6) and Stacey E. Rutledge for helpful comments. This work was supported by the National Institutes of Health.

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Journal Article↗