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1.  The Intrinsically Disordered Regions of the Drosophila melanogaster Hox Protein Ultrabithorax Select Interacting Proteins Based on Partner Topology 
PLoS ONE  2014;9(10):e108217.
Interactions between structured proteins require a complementary topology and surface chemistry to form sufficient contacts for stable binding. However, approximately one third of protein interactions are estimated to involve intrinsically disordered regions of proteins. The dynamic nature of disordered regions before and, in some cases, after binding calls into question the role of partner topology in forming protein interactions. To understand how intrinsically disordered proteins identify the correct interacting partner proteins, we evaluated interactions formed by the Drosophila melanogaster Hox transcription factor Ultrabithorax (Ubx), which contains both structured and disordered regions. Ubx binding proteins are enriched in specific folds: 23 of its 39 partners include one of 7 folds, out of the 1195 folds recognized by SCOP. For the proteins harboring the two most populated folds, DNA-RNA binding 3-helical bundles and α-α superhelices, the regions of the partner proteins that exhibit these preferred folds are sufficient for Ubx binding. Three disorder-containing regions in Ubx are required to bind these partners. These regions are either alternatively spliced or multiply phosphorylated, providing a mechanism for cellular processes to regulate Ubx-partner interactions. Indeed, partner topology correlates with the ability of individual partner proteins to bind Ubx spliceoforms. Partners bind different disordered regions within Ubx to varying extents, creating the potential for competition between partners and cooperative binding by partners. The ability of partners to bind regions of Ubx that activate transcription and regulate DNA binding provides a mechanism for partners to modulate transcription regulation by Ubx, and suggests that one role of disorder in Ubx is to coordinate multiple molecular functions in response to tissue-specific cues.
PMCID: PMC4186791  PMID: 25286318
Disconnected Interacting Protein 1 (DIP1), a member of the double-stranded RNA-binding protein family based on amino acid sequence, was shown previously to form complexes with multiple transcription factors in Drosophila melanogaster. To explore this protein further, we have undertaken sedimentation equilibrium experiments that demonstrate that DIP1-c (longest isoform of DIP1) is a dimer in solution, a characteristic common to other members of the dsRNA-binding protein family. The closest sequence identity for DIP1 is found within the dsRBD sequences of RNA editase enzymes. Consistent with this role, we demonstrate binding of DIP1-c to a potential physiological RNA target: pre-tRNA. In addition, DIP1-c was shown to interact with ADAT, a tRNA deaminase that presumably modifies pre-tRNAs. From these data, we hypothesize that DIP1 may serve an integrator role by binding its dsRNA ligand and recruiting protein partners for the appropriate metabolism of the bound RNA.
PMCID: PMC3205248  PMID: 21971547
dsRNA-binding protein; DIP1; ADAT; high affinity; tRNA; Gel retardation
3.  Altering Residues N125 and D149 Impacts Sugar Effector Binding and Allosteric Parameters in Escherichia coli Lactose Repressor 
Biochemistry  2011;50(42):9002-9013.
Lactose repressor protein (LacI), a negative transcriptional regulator in Escherichia coli, relies on an allosteric conformational change for its function. The LacI effector isopropyl-β,D-thiogalactoside (IPTG) promotes this allosteric response and engages the side chains of residues N125 and D149 based on the crystallographic structure of LacI·IPTG. Targeted molecular dynamics (TMD) simulations have indicated involvement of these side chains during the protein structural changes in response to inducer binding. To examine this region further, we applied stochastic boundary molecular dynamics (SBMD) simulation and identified a transient interaction between residues N125 and D149. Based on these data, we introduced substitutions for either/both residues and analyzed their impact on protein function. The substitutions utilized were alanine to preclude hydrogen bonding or cysteine to allow disulfide bond formation, which was not observed for N125C/D149C. Minimal impacts were observed on operator affinity for all substitutions, but D149C, N125A/D149A and N125C/D149C bound to IPTG with 5-8 fold lower affinity than wild-type LacI and exhibited decreased allosteric amplitude (KRI/O/KR/O). Of interest, the double mutants did not exhibit an allosteric response to an alternate inducer, 2-phenylethyl-β,D-galactoside (PhEG), despite demonstration of PhEG binding. Further, the presence of the anti-inducer, o-nitrophenyl-β,D-fucoside (ONPF), enhanced operator affinity for wild-type LacI and all other mutant proteins examined, but behaved as an inducer for N125A/D149A, decreasing operator binding affinity. These results confirm the role of residues 125 and 149 in ligand binding and allosteric response and illustrate how readily the function of a regulatory protein can be altered.
PMCID: PMC3202982  PMID: 21928765
LacI allostery; sugar specificity; ligand binding; structure/function
4.  Positions 94–98 of the lactose repressor N-subdomain monomer•monomer interface are critical for allosteric communication† 
Biochemistry  2010;49(39):8636-8645.
The central region of the LacI N-subdomain monomer•monomer interface includes residues K84, V94, V95, V96, S97, and M98. The side chains of these residues line the β-strands at this interface and interact to create a network of hydrophobic, charged, and polar interactions that significantly rearranges in different functional states of LacI. Prior work showed that converting K84 to an apolar residue or converting V96 to an acidic residue impedes the allosteric response to inducer. Thus, we postulated that a disproportionate number of substitutions in this region of the monomer•monomer interface would alter the complex features of the LacI allosteric response. To explore this hypothesis, acidic, basic, polar, and apolar mutations were introduced at positions 94–98. Despite their varied locations along the β-strands that flank the interface, ~70% of the mutations impact allosteric behavior, with the most significant effects found for charged substitutions. Of note, many of the LacI variants with minor functional impact exhibited altered stability to urea denaturation. The results confirm the critical role of amino acids 94–98 and indicate that this N-subdomain interface forms a primary pathway in LacI allosteric response.
PMCID: PMC3006071  PMID: 20804152
LacI; allostery; conformational change; ligand binding; structure/function
Disconnected Interacting Protein 1 (DIP1) appears from sequence analysis and preliminary binding studies to be a member of the dsRNA-binding protein family. Of interest, DIP1 was shown previously to interact with and influence multiple proteins involved in transcription regulation in Drosophila melanogaster. We show here that the longest isoform of this protein, DIP1-c, exhibits a 500-fold preference for dsRNA over dsDNA of similar nucleotide sequence. Further, DIP1-c demonstrated very high affinity for a subset of dsRNA ligands, with binding in the picomolar range for VA1 RNA and miR-iab-4 precursor stem-loop, a potential physiological RNA target involved in regulating expression of its protein partner, Ultrabithorax.
PMCID: PMC2931317  PMID: 20643095
dsRNA-binding protein; DIP1; gel retardation; high affinity; adenovirus VA1 RNA; iab-4 miRNA
6.  Media composition influences yeast one- and two-hybrid results 
Although yeast two-hybrid experiments are commonly used to identify protein interactions, the frequent occurrence of false negatives and false positives hampers data interpretation. Using both yeast one-hybrid and two-hybrid experiments, we have identified potential sources of these problems: the media preparation protocol and the source of the yeast nitrogen base may not only impact signal range but also effect whether a result appears positive or negative. While altering media preparation may optimize signal differences for individual experiments, media preparation must be reported in detail to replicate studies and accurately compare results from different experiments.
PMCID: PMC3177868  PMID: 21843345
Yeast one-hybrid; yeast two-hybrid; protein-protein interaction; accuracy; false positive; false negative
7.  New research resources at the Bloomington Drosophila Stock Center 
Fly  2010;4(1):88-91.
The Bloomington Drosophila Stock Center (BDSC) is a primary source of Drosophila stocks for researchers all over the world. It houses over 27,000 unique fly lines and distributed over 160,000 samples of these stocks this past year. This report provides a brief overview of significant recent events at the BDSC with a focus on new stock sets acquired in the past year, including stocks for φC31 transformation, RNAi knockdown of gene expression, and SNP and quantitative trait loci discovery. We also describe additions to sets of insertions and molecularly defined chromosomal deficiencies, the creation of a new Deficiency Kit, and planned additions of X chromosome duplication sets.
PMCID: PMC2997732  PMID: 20160480
Bloomington Drosophila Stock Center; stocks; insertions; deletions; deficiency kit; duplications; C31; RNAi; Minos; sequenced inbred strains
Journal of molecular biology  2009;390(4):760-774.
In developing bilaterans, the Hox transcription factor family regulates batteries of downstream genes to diversify serially repeated units. Given Hox homeodomains bind a wider array of DNA binding sites in vitro than are regulated by the full-length protein in vivo, regions outside the homeodomain must aid DNA site selection. Indeed, we find affinity for disparate DNA sequences varies less than 3-fold for the homeodomain isolated from the Drosophila Hox protein Ultrabithorax Ia (UbxHD), whereas for the full-length protein (UbxIa) affinity differs by more than 10-fold. The rank order of preferred DNA sequences also differs, further demonstrating distinct DNA binding preferences. The increased specificity of UbxIa can be partially attributed to the I1 region, which lies adjacent to the homeodomain and directly impacts binding energetics. Each of three segments within I1 – the Extradenticle-binding YPWM motif, the 6 amino acids immediately N-terminal to this motif, and the 8 amino acids abutting the YPWM C-terminus – uniquely contribute to DNA specificity. Combination of these regions synergistically modifies DNA binding to further enhance specificity. Intriguingly, the presence of the YPWM motif in UbxIa inhibits DNA binding only to Ubx•Extradenticle heterodimer binding sites, potentially functioning in vivo to prevent Ubx monomers from binding and misregulating heterodimer target genes. However, removal of the surrounding region allows the YPWM motif to also inhibit binding to Hox-only recognition sequences. Despite a modular domain design for Hox proteins, these results suggest that multiple Hox protein regions form a network of regulatory interactions that coordinate context-and gene-specific responses. Since most non-homeodomain regions are not conserved between Hox family members, these regulatory interactions have the potential to diversify binding by the highly homologous Hox homeodomains.
PMCID: PMC2739810  PMID: 19481089
Hox; DNA binding; homeodomain; YPWM; hexapeptide motif
9.  Flexibility in the Inducer Binding Region is Crucial for Allostery in the Escherichia coli Lactose Repressor† 
Biochemistry  2009;48(22):4988-4998.
Lactose repressor protein (LacI) utilizes an allosteric mechanism to regulate transcription in E. coli, and the transition between inducer- and operator-bound states has been simulated by targeted molecular dynamics (TMD). The side chains of amino acids 149 and 193 interact and were predicted by TMD simulation to play a critical role in the early stages of the LacI conformational change. D149 contacts IPTG directly, and variations at this site provide the opportunity to dissect its role in inducer binding and signal transduction. Single mutants at D149 or S193 exhibit minimal change in operator binding, and alterations in inducer binding parallel changes in operator release, indicating normal allosteric response. The observation that the double mutant D149A/S193A exhibits wild-type properties excludes the requirement for inter-residue hydrogen bond formation in the allosteric response. The double mutant D149C/S193C purified from cell extracts shows decreased sensitivity to inducer binding, while retaining wild-type binding affinities and kinetic constants for both operator and inducer. By manipulating cysteine oxidation, we show that the more reduced state of D149C/S193C responds to inducer more similarly to wild-type protein, whereas the more oxidized state displays diminished inducer sensitivity. These features of D149C/S193C indicate that the novel disulfide bond formed in this mutant impedes the allosteric transition, consistent with the role of this region predicted by TMD simulation. Together, these results establish the requirement for flexibility of spatial relationship between D149 and S193 rather than a specific D149-S193 interaction in the LacI allosteric response to inducer.
PMCID: PMC2772868  PMID: 19368358
10.  Allostery in the LacI/GalR Family: Variations on a Theme 
Current opinion in microbiology  2009;12(2):129-137.
The lactose repressor protein (LacI) was among the very first genetic regulatory proteins discovered, and more than 1000 members of the bacterial LacI/GalR family are now identified. LacI has been the prototype for understanding how transcription is controlled using small metabolites to modulate protein association with specific DNA sites. This understanding has been greatly expanded by the study of other LacI/GalR homologues. A general picture emerges in which the conserved fold provides a scaffold for multiple types of interactions —including oligomerization, small molecule binding, and protein•protein binding — that in turn influence target DNA binding and thereby regulate mRNA production. Although many different functions have evolved from this basic scaffold, each homologue retains functional flexibility: For the same protein, different small molecules can have disparate impact on DNA binding and hence transcriptional outcome. In turn, binding to alternative DNA sequences may impact the degree of allosteric response. Thus, this family exhibits a symphony of variations by which transcriptional control is achieved.
PMCID: PMC2688824  PMID: 19269243
11.  Extrinsic Interactions Dominate Helical Propensity in Coupled Binding and Folding of Lactose Repressor Protein Hinge Helix† 
Biochemistry  2006;45(18):5896-5906.
A significant number of eukaryotic regulatory proteins are predicted to have disordered regions. Many of these proteins bind DNA, which may serve as a template for protein folding. Similar behavior is seen in the prokaryotic LacI/GalR family of proteins that couple hinge-helix folding with DNA binding. These hinge regions form short α-helices when bound to DNA, but appear to be disordered in other states. An intriguing question is whether and to what degree intrinsic helix propensity contributes to the function of these proteins. In addition to its interaction with operator DNA, the LacI hinge helix interacts with the hinge helix of the homodimer partner as well as to the surface of the inducer-binding domain. To explore the hierarchy of these interactions, we made a series of substitutions in the LacI hinge helix at position 52, the only site in the helix that does not interact with DNA and/or the inducer-binding domain. The substitutions at V52 have significant effects on operator binding affinity and specificity, and several substitutions also impair functional communication with the inducer-binding domain. Results suggest that helical propensity of amino acids in the hinge region alone does not dominate function; helix-helix packing interactions appear to also contribute. Further, the data demonstrate that variation in operator sequence can overcome side chain effects on hinge helix folding and/or hinge•hinge interactions. Thus, this system provides a direct example whereby an extrinsic interaction (DNA binding) guides internal events that influence folding and functionality.
PMCID: PMC2701349  PMID: 16669632
LacI; helical propensity; allostery; DNA binding
12.  Ligand-Induced Conformational Changes and Conformational Dynamics in the Solution Structure of the Lactose Repressor Protein 
Journal of molecular biology  2007;376(2):466-481.
We present here the results of a series of small-angle X-ray scattering studies aimed at understanding the role of conformational changes and structural flexibility in DNA binding and allosteric signaling in a bacterial transcription regulator, Lactose repressor protein (LacI). Experiments were designed to detect possible conformational changes that occur when LacI binds either DNA or the inducer IPTG, or both. Our studies included the native LacI dimer of homodimers and a dimeric variant (R3), enabling us to probe conformational changes within the homodimers and distinguish them from those involving changes in the homodimer-homodimer relationships. The scattering data indicate that removal of operator DNA (oDNA) from R3 results in an unfolding and extension of the hinge-helix that connects the LacI regulatory and DNA-binding domains. In contrast, only very subtle conformational changes occur in the R3 dimer-oDNA complex upon IPTG binding, indicative of small adjustments in the orientations of domains and/or sub-domains within the structure. The binding of IPTG to native (tetrameric) LacI-oDNA complexes also appears to facilitate a modest change in the average homodimer-homodimer disposition. Notably, the crystal structure of the native LacI-oDNA complex differs significantly from the average solution conformation. The solution scattering data are best-fit by an ensemble of structures that includes (1) ~60% of the V-shaped dimer-of-homodimers observed in the crystal structure, and (2) ~40% of molecules with more “open” forms, such as those generated when the homodimers move with respect to each other about the tetramerization domain. In gene regulation, such a flexible LacI would be beneficial for the interaction of its two DNA binding domains, positioned at the tips of the V, with the required two of three LacI operators needed for full repression.
PMCID: PMC2430094  PMID: 18164724
LacI; allostery; small; angle X; ray scattering; solution structure

Results 1-12 (12)