Solution structure of the DNA-binding domain of Cd2-GAL4 from S. cerevisiae

Protein structure determination in human cells by in-cell NMR and a reporter system to optimize protein delivery or transexpression

Most experimental methods for structural biology proceed in vitro and therefore the contribution of the intracellular environment on protein structure and dynamics is absent. Studying proteins at atomic resolution in living mammalian cells has been elusive due to the lack of methodologies. In-cell nuclear magnetic resonance spectroscopy (in-cell NMR) is an emerging technique with the power to do so. Here, we improved current methods of in-cell NMR by the development of a reporter system that allows monitoring the delivery of exogenous proteins into mammalian cells, a process that we called here "transexpression". The reporter system was used to develop an efficient protocol for in-cell NMR which enables spectral acquisition with higher quality for both disordered and folded proteins. With this method, the 3D atomic resolution structure of the model protein GB1 in human cells was determined with a backbone root-mean-square deviation (RMSD) of 1.1 Å.

Zinc finger structure determination by NMR: Why zinc fingers can be a handful

Zinc fingers can be loosely defined as protein domains containing one or more tetrahedrally-co-ordinated zinc ions whose role is to stabilise the structure rather than to be involved in enzymatic chemistry; such zinc ions are often referred to as "structural zincs". Although structural zincs can occur in proteins of any size, they assume particular significance for very small protein domains, where they are often essential for maintaining a folded state. Such small structures, that sometimes have only marginal stability, can present particular difficulties in terms of sample preparation, handling and structure determination, and early on they gained a reputation for being resistant to crystallisation. As a result, NMR has played a more prominent role in structural studies of zinc finger proteins than it has for many other types of proteins. This review will present an overview of the particular issues that arise for structure determination of zinc fingers by NMR, and ways in which these may be addressed.

In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity

Despite interest in associating polymorphisms with clinical or experimental phenotypes, functional interpretation of mutation data has lagged behind generation of data from modern high-throughput techniques and the accurate prediction of the molecular impact of a mutation remains a non-trivial task. We present here an integrated knowledge-driven computational workflow designed to evaluate the effects of experimental and disease missense mutations on protein structure and interactions. We exemplify its application with analyses of saturation mutagenesis of DBR1 and Gal4 and show that the experimental phenotypes for over 80% of the mutations correlate well with predicted effects of mutations on protein stability and RNA binding affinity. We also show that analysis of mutations in VHL using our workflow provides valuable insights into the effects of mutations, and their links to the risk of developing renal carcinoma. Taken together the analyses of the three examples demonstrate that structural bioinformatics tools, when applied in a systematic, integrated way, can rapidly analyse a given system to provide a powerful approach for predicting structural and functional effects of thousands of mutations in order to reveal molecular mechanisms leading to a phenotype. Missense or non-synonymous mutations are nucleotide substitutions that alter the amino acid sequence of a protein. Their effects can range from modifying transcription, translation, processing and splicing, localization, changing stability of the protein, altering its dynamics or interactions with other proteins, nucleic acids and ligands, including small molecules and metal ions. The advent of high-throughput techniques including sequencing and saturation mutagenesis has provided large amounts of phenotypic data linked to mutations. However, one of the hurdles has been understanding and quantifying the effects of a particular mutation, and how they translate into a given phenotype. One approach to overcome this is to use robust, accurate and scalable computational methods to understand and correlate structural effects of mutations with disease.

The GAL4 System: A Versatile System for the Manipulation and Analysis of Gene Expression

Since its introduction in 1993, the GAL4 system has become an essential part of the Drosophila geneticist's toolkit. Widely used to drive gene expression in a multitude of cell- and tissue-specific patterns, the system has been adapted and extended to form the basis of many modern tools for the manipulation of gene expression in Drosophila and other model organisms.

Gal3 Binds Gal80 Tighter than Gal1 Indicating Adaptive Protein Changes Following Duplication

Derived from the yeast whole-genome duplication, Saccharomyces cerevisiae GAL1 and GAL3 encode the catabolic enzyme galactokinase (Gal1) and its transcriptional coinducer (Gal3), whereas the ancestral, preduplicated GAL1 gene performed both functions. Previous studies indicated that divergence was primarily driven by changes in upstream promoter elements, and changes in GAL3's coding region are assumed to be the result of drift. We show that replacement of GAL3's open-reading-frame with GAL1's results in an extended lag phase upon switching to growth on galactose with up to 2.5-fold differences in the initial cell masses. Accordingly, the binding affinity of Gal3 to Gal80 was found to be greater than 10-folds higher than that of Gal1, with both a higher association rate (ka) and lower dissociation (kd) rate. Thus, while changes in the noncoding, regulatory regions were the initial driving force for GAL3's subfunctionalization as a coinducer, adaptive changes in the protein sequence seem to have followed.

¹¹³Cd NMR experiments reveal an unusual metal cluster in the solution structure of the yeast splicing protein Bud31p

Establishing the binding topology of structural zinc ions in proteins is an essential part of their structure determination by NMR spectroscopy. Using (113)Cd NMR experiments with (113)Cd-substituted samples is a useful approach but has previously been limited mainly to very small protein domains. Here we used (113)Cd NMR spectroscopy during structure determination of Bud31p, a 157-residue yeast protein containing an unusual Zn3Cys9 cluster, demonstrating that recent hardware developments make this approach feasible for significantly larger systems.

113Cd NMR Experiments Reveal an Unusual Metal Cluster in the Solution Structure of the Yeast Splicing Protein Bud31p

Establishing the binding topology of structural zinc ions in proteins is an essential part of their structure determination by NMR spectroscopy. Using ¹¹³Cd NMR experiments with ¹¹³Cd‐substituted samples is a useful approach but has previously been limited mainly to very small protein domains. Here we used ¹¹³Cd NMR spectroscopy during structure determination of Bud31p, a 157‐residue yeast protein containing an unusual Zn₃Cys₉ cluster, demonstrating that recent hardware developments make this approach feasible for significantly larger systems.

Acetylation of the transcriptional repressor Ume6p allows efficient promoter release and timely induction of the meiotic transient transcription program in yeast

Differentiation programs require strict spatial and temporal control of gene transcription. Genes expressed during meiotic development in Saccharomyces cerevisiae display transient induction and repression. Early meiotic gene (EMG) repression during mitosis is achieved by recruiting both histone deacetylase and chromatin remodeling complexes to their promoters by the zinc cluster DNA binding protein Ume6p. Ume6p repression is relieved by ubiquitin-mediated destruction that is stimulated by Gcn5p-induced acetylation. In this report, we demonstrate that Gcn5p acetylation of separate lysines within the zinc cluster domain negatively impacts Ume6p DNA binding. Mimicking lysine acetylation using glutamine substitution mutations decreased Ume6p binding efficiency and resulted in partial derepression of Ume6p-regulated genes. Consistent with this result, molecular modeling predicted that these lysine side chains are adjacent to the DNA phosphate backbone, suggesting that acetylation inhibits Ume6p binding by electrostatic repulsion. Preventing acetylation did not impact final EMG induction levels during meiosis. However, a delay in EMG induction was observed, which became more severe in later expression classes, ultimately resulting in delayed and reduced execution of the meiotic nuclear divisions. These results indicate that Ume6p acetylation ensures the proper timing of the transient transcription program during meiotic development.

The Gal3p transducer of the GAL regulon interacts with the Gal80p repressor in its ligand-induced closed conformation

A wealth of genetic information and some biochemical analysis have made the GAL regulon of the yeast Saccharomyces cerevisiae a classic model system for studying transcriptional activation in eukaryotes. Galactose induces this transcriptional switch, which is regulated by three proteins: the transcriptional activator Gal4p, bound to DNA; the repressor Gal80p; and the transducer Gal3p. We showed previously that NADP appears to act as a trigger to kick the repressor off the activator. Sustained activation involves a complex of the transducer Gal3p and Gal80p mediated by galactose and ATP. We solved the crystal structure of the complex of Gal3p-Gal80p with α-D-galactose and ATP to 2.1 Å resolution. The interaction between the proteins occurs only when Gal3p is in a "closed" state induced by ligand binding. The structure of the complex provides a rationale for the phenotypes of several well-known Gal80p and Gal3p mutants as well as the lack of galactokinase activity of Gal3p.

Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases

The N-end rule pathway is a regulated proteolytic system that targets proteins containing destabilizing N-terminal residues (N-degrons) for ubiquitination and proteasomal degradation in eukaryotes. The N-degrons of type 1 substrates contain an N-terminal basic residue that is recognized by the UBR box domain of the E3 ubiquitin ligase UBR1. We describe structures of the UBR box of Saccharomyces cerevisiae UBR1 alone and in complex with N-degron peptides, including that of the cohesin subunit Scc1, which is cleaved and targeted for degradation at the metaphase-anaphase transition. The structures reveal a previously unknown protein fold that is stabilized by a novel binuclear zinc center. N-terminal arginine, lysine or histidine side chains of the N-degron are coordinated in a multispecific binding pocket. Unexpectedly, the structures together with our in vitro biochemical and in vivo pulse-chase analyses reveal a previously unknown modulation of binding specificity by the residue at position 2 of the N-degron.

Cadmium(II) complex formation with cysteine and penicillamine

The complex formation between cadmium(II) and the ligands cysteine (H(2)Cys) and penicillamine (H(2)Pen = 3,3'-dimethylcysteine) in aqueous solutions, having C(Cd(II)) approximately 0.1 mol dm(-3) and C(H(2)L) = 0.2-2 mol dm(-3), was studied at pH = 7.5 and 11.0 by means of (113)Cd NMR and Cd K- and L(3)-edge X-ray absorption spectroscopy. For all cadmium(II)-cysteine molar ratios, the mean Cd-S and Cd-(N/O) bond distances were found in the ranges 2.52-2.54 and 2.27-2.35 A, respectively. The corresponding cadmium(II)-penicillamine complexes showed slightly shorter Cd-S bonds, 2.50-2.53 A, but with the Cd-(N/O) bond distances in a similar wide range, 2.28-2.33 A. For the molar ratio C(H(2)L)/C(Cd(II)) = 2, the (113)Cd chemical shifts, in the range 509-527 ppm at both pH values, indicated complexes with distorted tetrahedral CdS(2)N(N/O) coordination geometry. With a large excess of cysteine (molar ratios C(H(2)Cys)/C(Cd(II)) >or= 10), complexes with CdS(4) coordination geometry dominate, consistent with the (113)Cd NMR chemical shifts, delta approximately 680 ppm at pH 7.5 and 636-658 ppm at pH 11.0, and their mean Cd-S distances were 2.53 +/- 0.02 A. At pH 7.5, the complexes are almost exclusively sulfur-coordinated as [Cd(S-cysteinate)(4)](n-), while at higher pH, the deprotonation of the amine groups promotes chelate formation. At pH 11.0, a minor amount of the [Cd(Cys)(3)](4-) complex with CdS(3)N coordination is formed. For the corresponding penicillamine solutions with molar ratios C(H(2)Pen)/C(Cd(II)) >or= 10, the (113)Cd NMR chemical shifts, delta approximately 600 ppm at pH 7.5 and 578 ppm at pH 11.0, together with the average bond distances, Cd-S 2.53 +/- 0.02 A and Cd-(N/O) 2.30-2.33 A, indicate that [Cd(penicillaminate)(3)](n-) complexes with chelating CdS(3)(N/O) coordination dominate already at pH 7.5 and become mixed with CdS(2)N(N/O) complexes at pH 11.0. The present study reveals differences between cysteine and penicillamine as ligands to the cadmium(II) ion that can explain why cysteine-rich metallothionines are capable of capturing cadmium(II) ions, while penicillamine, clinically useful for treating the toxic effects of mercury(II) and lead(II) exposure, is not efficient against cadmium(II) poisoning.

Structural basis for dimerization in DNA recognition by Gal4

Gal4 is a Zn2Cys6 binuclear cluster containing transcription factor that binds DNA as a homodimer and can activate transcription by interacting with the mutant Gal11P protein. Although structures have been reported of the Gal4 dimerization domain and the binuclear cluster domain bound to DNA as a dimer, the structure of the "complete" Gal4 dimer bound to DNA has not previously been described. Here we report the structure of a complete Gal4 dimer bound to DNA and additional biochemical studies to address the molecular basis for Gal4 dimerization in DNA binding. We find that Gal4 dimerization on DNA is mediated by an intertwined helical bundle that deviates significantly from the solution NMR structure of the free dimerization domain. Associated biochemical studies show that the dimerization domain of Gal4 is important for DNA binding and protein thermostability. We also map the interaction surface of the Gal4 dimerization domain with Gal11P.

Eukaryotic class 1 translation termination factor eRF1 − the NMR structure and dynamics of the middle domain involved in triggering ribosome-dependent peptidyl-tRNA hydrolysis

The eukaryotic class 1 polypeptide chain release factor is a three-domain protein involved in the termination of translation, the final stage of polypeptide biosynthesis. In attempts to understand the roles of the middle domain of the eukaryotic class 1 polypeptide chain release factor in the transduction of the termination signal from the small to the large ribosomal subunit and in peptidyl-tRNA hydrolysis, its high-resolution NMR structure has been obtained. The overall fold and the structure of the beta-strand core of the protein in solution are similar to those found in the crystal. However, the orientation of the functionally critical GGQ loop and neighboring alpha-helices has genuine and noticeable differences in solution and in the crystal. Backbone amide protons of most of the residues in the GGQ loop undergo fast exchange with water. However, in the AGQ mutant, where functional activity is abolished, a significant reduction in the exchange rate of the amide protons has been observed without a noticeable change in the loop conformation, providing evidence for the GGQ loop interaction with water molecule(s) that may serve as a substrate for the hydrolytic cleavage of the peptidyl-tRNA in the ribosome. The protein backbone dynamics, studied using 15N relaxation experiments, showed that the GGQ loop is the most flexible part of the middle domain. The conformational flexibility of the GGQ and 215-223 loops, which are situated at opposite ends of the longest alpha-helix, could be a determinant of the functional activity of the eukaryotic class 1 polypeptide chain release factor, with that helix acting as the trigger to transmit the signals from one loop to the other.

The cotton fiber zinc-binding domain of cellulose synthase A1 from Gossypium hirsutum displays rapid turnover in vitro and in vivo

Little is known about the assembly and turnover of cellulose synthase complexes commonly called rosettes. Recent work indicates that rosette assembly could involve the dimerization of CesA (cellulose synthase catalytic subunit) proteins regulated by the redox state of the CesA zinc-binding domain (ZnBD). Several studies in the 1980s led to the suggestion that synthase complexes may have very short half-lives in vivo, but no recent work has directly addressed this issue. In the present work, we show that the half-life of cotton fiber GhCesA1 protein is <30 min in vivo, far less than the average membrane protein. We also show that the reduced monomer of GhCesA1 ZnBD is rapidly degraded when exposed to cotton fiber extracts, whereas the oxidized dimer is resistant to degradation. Low rates of degradation activity were detected in vitro by using extracts from fibers harvested during primary cell-wall formation, but activity increased markedly during transition to secondary cell-wall synthesis. In vitro degradation of reduced GhCesA1 ZnBD is inhibited by proteosome inhibitor MG132 and also by E64 and EGTA, suggesting that proteolysis is initiated by cysteine protease activity rather than the proteosome. We used a yeast two-hybrid system to identify a putative cotton fiber metallothionein and to confirm it as a protein that could interact with the GhCesA1 ZnBD. A model is proposed wherein active cellulose synthase complexes contain CesA proteins in dimerized form, and turnover and degradation of the complexes are mediated through reductive zinc insertion by metallothionein and subsequent proteolysis involving a cysteine protease.

Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations

We present refinements of the SIBFA molecular mechanics procedure to represent the intermolecular interaction energies of Zn(II). The two first-order contributions, electrostatic (E(MTP)), and short-range repulsion (E(rep)), are refined following the recent developments due to Piquemal et al. (Piquemal et al. J Phys Chem A 2003, 107, 9800; and Piquemal et al., submitted). Thus, E(MTP) is augmented with a penetration component, E(pen), which accounts for the effects of reduction in electronic density of a given molecular fragment sensed by another interacting fragment upon mutual overlap. E(pen) is fit in a limited number of selected Zn(II)-mono-ligated complexes so that the sum of E(MTP) and E(pen) reproduces the Coulomb contribution E(c) from an ab initio Hartree-Fock energy decomposition procedure. Denoting by S, the overlap matrix between localized orbitals on the interacting monomers, and by R, the distance between their centroids, E(rep) is expressed by a S(2)/R term now augmented with an S(2)/R(2) one. It is calibrated in selected monoligated Zn(II) complexes to fit the corresponding exchange repulsion E(exch) from ab initio energy decomposition, and no longer as previously the difference between (E(c) + E(exch)) and E(MTP). Along with the reformulation of the first-order contributions, a limited recalibration of the second-order contributions was carried out. As in our original formulation (Gresh, J Comput Chem 1995, 16, 856), the Zn(II) parameters for each energy contribution were calibrated to reproduce the radial behavior of its ab initio HF counterpart in monoligated complexes with N, O, and S ligands. The SIBFA procedure was subsequently validated by comparisons with parallel ab initio computations on several Zn(II) polyligated complexes, including binuclear Zn(II) complexes as in models for the Gal4 and beta-lactamase metalloproteins. The largest relative error with respect to the RVS computations is 3%, and the ordering in relative energies of competing structures reproduced even though the absolute numerical values of the ab initio interaction energies can be as large as 1220 kcal/mol. A term-to-term identification of the SIBFA contributions to their ab initio counterparts remained possible even for the largest sized complexes.

Dynamics and Metal Exchange Properties of C4C4 RING Domains from CNOT4 and the p44 Subunit of TFIIH

Zinc fingers are small structured protein domains that require the coordination of zinc for a stable tertiary fold. Together with FYVE and PHD, the RING domain forms a distinct class of zinc-binding domains, where two zinc ions are ligated in a cross-braced manner, with the first and third pairs of ligands coordinating one zinc ion, while the second and fourth pairs ligate the other zinc ion. To investigate the relationship between the stability and dynamic behaviour of the domains and the stability of the metal-binding site, we studied metal exchange for the C4C4 RING domains of CNOT4 and the p44 subunit of TFIIH. We found that Zn(2+)-Cd(2+) exchange is different between the two metal-binding sites in the C4C4 RING domains of the two proteins. In order to understand the origins of these distinct exchange rates, we studied the backbone dynamics of both domains in the presence of zinc and of cadmium by NMR spectroscopy. The differential stability of the two metal-binding sites in the RING domains, as reflected by the different metal exchange rates, can be explained by a combination of accessibility and an electrostatic ion interaction model. A greater backbone flexibility for the p44 RING domain as compared to CNOT4 may be related to the distinct types of protein-protein interactions in which the two C4C4 RING domains are involved.

Tumor-specific adenoviral gene therapy: transcriptional repression of gene expression by utilizing p53-signal transduction pathways

Adenoviral gene expression that is repressed by p53 in nontransformed cells could provide a tumor-specific gene therapy approach for a large subset of tumors. Adenoviral infection in vivo induces stabilization of p53, which can be utilized for a strategy that includes p53-dependent expression of a transcriptional repressor and a target promoter,which is highly susceptible for transcriptional repression. Therefore, we constructed different versions of CMV-promoters (CMVgal) with binding sites for GAL4-DBD and investigated 11 GAL4-DBD fusion proteins to elucidate the most effective repressor domain to silence CMVgal activity. The transcriptional repressor GAL4-KRAB-A under control of a p53-dependent promoter facilitates strong CMVgal-mediated gene expression specifically in p53 mutant cells by a double-recombinant adenoviral vector (Ad-RGCdR). GAL4-KRAB-A mediates strong transcriptional repression of Ad-RGCdR in p53 wild-type cells, which could be further enhanced by preactivation of p53-signalling following low-dose chemotherapy prior to adenoviral infection. By utilizing p53 signalling involved in chemotherapy and adenoviral infection, more than 99% of Ad-RGCdR gene expression could be repressed in p53 wild-type cells. Controlled gene expression from CMVgal promoters by transcriptional repression utilizing functional p53 signalling thus provides a very effective tool for tumor-specific adenoviral gene therapy.

Complex interplay among regulators of drug resistance genes in Saccharomyces cerevisiae

The Gal4p family of yeast zinc cluster proteins comprises regulators of multidrug resistance genes. For example, Pdr1p and Pdr3p bind as homo- or heterodimers to pleiotropic drug response elements (PDREs) found in promoters of target genes. Other zinc cluster activators of multidrug resistance genes include Stb5p and Yrr1p. To better understand the interplay among these activators, we have performed native co-immunoprecipitation experiments using strains expressing tagged zinc cluster proteins from their natural chromosomal locations. Interestingly, Stb5p is found predominantly as a Pdr1p heterodimer and shows little homodimerization. No interactions of Stb5p with Pdr3p or Yrr1p could be detected in our assays. In contrast to Stb5p, Yrr1p is only detected as a homodimer. Similar results were obtained using glutathione S-transferase pull-down assays. Importantly, the purified DNA binding domains of Stb5p and Pdr1p bound to a PDRE as heterodimers in vitro. These results suggest that the DNA binding domains of Pdr1p and Stb5p are sufficient for heterodimerization. Our data demonstrate a complex interplay among these activators and suggest that Pdr1p is a master drug regulator involved in recruiting other zinc cluster proteins to fine tune the regulation of multidrug resistance genes.

Nuclear magnetic resonance structures of the zinc finger domain of human DNA polymerase-α

The carboxy terminus of the human DNA polymerase-alpha contains a zinc finger motif. Three-dimensional structures of this motif containing 38 amino acid residues, W L I C E E P T C R N R T R H L P L Q F S R T G P L C P A C M K A T L Q P E, were determined by nuclear magnetic resonance (NMR) spectroscopy. The structures reveal an alpha-helix-like domain at the amino terminus, extending 13 residues from L2 through H15 with an interruption at the sixth residue. The helix region is followed by three turns (H15-L18, T23-L26 and L26-A29), all of which involve proline. The first turn appears to be type III, judging by the dihedral angles. The second and third turns appear to be atypical. A second, shorter helix is formed at the carboxy terminus extending from C30 through L35. A fourth type III turn starting at L35 was also observed in the structure. Proline serves as the third residue of all the turns. Four cysteine residues, two located at the beginning of the helix at the N-terminus and two at the carboxy end, are coordinated to Zn(II), facilitating the formation of a loop. One of the cysteines at the carboxy terminus is part of the atypical turn, while the other is the part of the short helix. These structural features are consistent with the circular dichroism (CD) measurements which indicate the presence of 45% helix, 11% beta turns and 19% non-ordered secondary structures. The zinc finger motif described here is different from those observed for C(4), C(2)H(2), and C(2)HC modules reported in the literature. In particular, polymerase-alpha structures exhibit helix-turn-helix motif while most zinc finger proteins show anti-parallel sheet and helix. Several residues capable of binding DNA, T, R, N, and H are located in the helical region. These structural features imply that the zinc finger motif is most likely involved in binding DNA prior to replication, presumably through the helical region. These results are discussed in the context of other eukaryotic and prokaryotic DNA polymerases belonging to the polymerase B family.

Progress toward an expanded eukaryotic genetic code

Expanding the eukaryotic genetic code to include unnatural amino acids with novel properties would provide powerful tools for manipulating protein function in eukaryotic cells. Toward this goal, a general approach with potential for isolating aminoacyl-tRNA synthetases that incorporate unnatural amino acids with high fidelity into proteins in Saccharomyces cerevisiae is described. The method is based on activation of GAL4-responsive HIS3, URA3, or lacZ reporter genes by suppression of amber codons in GAL4. The optimization of GAL4 reporters is described, and the positive and negative selection of active Escherichia coli tyrosyl-tRNA synthetase (EcTyrRS)/tRNA(CUA) is demonstrated. Importantly, both selections can be performed on a single cell and with a range of stringencies. This method will facilitate the isolation of a range of aminoacyl-tRNA synthetase (aaRS)/tRNA(CUA) activities from large libraries of mutant synthetases.

Induced folding of the U2AF35 RRM upon binding to U2AF65

The human essential splicing factor U2AF (U2 auxiliary factor) consists of 35 and 65 kDa subunits which form a highly stable heterodimer in solution. Copurification of the recombinant U2AF35 RNA recognition motif (U2AF35 RRM) and full-length U2AF65 yields a soluble and functionally active minimal U2AF heterodimer. Recombinant U2AF35 RRM protein free and in complex with three different regions of U2AF65 was characterized by nuclear magnetic resonance spectroscopy. We found that the recombinant U2AF35 RRM is unstructured in solution but its tertiary structure is induced upon binding to U2AF65. This interaction is mediated by the N-terminal proline-rich region of U2AF65 and does not involve the U2AF65 RRMs.

Evaluation of strategies for the intracellular delivery of proteins

PURPOSE

The intracellular delivery of functionally active protein represents an important emerging strategy for laboratory investigation and therapeutic applications. Although a number of promising approaches for protein delivery have been developed, thus far there has been no attempt to compare the merits of the various deliver technologies. This issue is addressed in the current study.

METHODS

In this study we utilize a sensitive luciferase reporter gene assay to provide unambiguous and quantitative evaluation of several strategies for the intracellular delivery of a biologically active protein comprised of the Gal4 DNA binding domain and the VP16 transactivating domain.

RESULTS

Both a cationic lipid supramolecular complex and a poly meric complex were able to effectively deliver the chimeric transcription factor to cultured cells. In addition, protein chimeras containing the Tat cell penetrating peptide, but not those containing the VP22 peptide, were somewhat effective in delivery.

CONCLUSIONS

Both supramolecular protein-carrier complexes and protein chimeras with certain cell penetrating peptides can support intracellular delivery of proteins. In the cell culture setting the supramolecular complexes are more effective, but their large size may present problems for in vivo applications.

Dimerization of cotton fiber cellulose synthase catalytic subunits occurs via oxidation of the zinc-binding domains

Cellulose synthase (CesA) proteins are components of CesA complexes (rosettes) and are thought to catalyze the chain elongation step in glucan polymerization. Little is understood about rosette assembly, including how CesAs interact with each other or with other components within the complexes. The first conserved region at the N terminus of plant CesA proteins contains two putative zinc fingers that show high homology to the RING-finger motif. We show that this domain in GhCesA1 can bind two atoms of Zn2+, as predicted by its structure. Analysis in the yeast two-hybrid system indicates that the N-terminal portions of cotton fiber GhCesA1 and GhCesA2 containing these domains can interact to form homo- or heterodimers. Although Zn(2+) binding occurs only when the protein is in the reduced form, biochemical analyses show that under oxidative conditions, the GhCesA1 zinc-finger domain and also the full-length protein dimerize via intermolecular disulfide bonds, indicating CesA dimerization can be regulated by redox state. We also provide evidence that the herbicide CGA 325'615 (Syngenta, Basel), which inhibits synthesis of crystalline cellulose and leads to a disruption of rosette architecture, may affect the oxidative state of the zinc-finger domain that is necessary for rosette stability. Taken together, these results support a model in which at least part of the process of rosette assembly and function may involve oxidative dimerization between CesA subunits.

Ethanol catabolism in Aspergillus nidulans: a model system for studying gene regulation

This article reviews our knowledge of the ethanol utilization pathway (alc system) in the hyphal fungus Aspergillus nidulans. We discuss the progress made over the past decade in elucidating the two regulatory circuits controlling ethanol catabolism at the level of transcription, specific induction, and carbon catabolite repression, and show how their interplay modulates the utilization of nutrient carbon sources. The mechanisms featuring in this regulation are presented and their modes of action are discussed: First, AlcR, the transcriptional activator, which demonstrates quite remarkable structural features and an original mode of action; second, the physiological inducer acetaldehyde, whose intracellular accumulation induces the alc genes and thereby a catabolic flux while avoiding intoxification; third, CreA, the transcriptional repressor mediating carbon catabolite repression in A. nidulans, which acts in different ways on the various alc genes; Fourth, the promoters of the structural genes for alcohol dehydrogenase (alcA) and aldehyde dehydrogenase (aldA) and the regulatory alcR gene, which exhibit exceptional strength compared to other genes of the respective classes. alc gene expression depends on the number and localization of regulatory cis-acting elements and on the particular interaction between the two regulator proteins, AlcR and CreA, binding to them. All these characteristics make the ethanol regulon a suitable system for induced expression of heterologous protein in filamentous fungi.

The solution structure of an AlcR-DNA complex sheds light onto the unique tight and monomeric DNA binding of a Zn(2)Cys(6) protein

BACKGROUND

In Aspergillus nidulans, the transcription activator AlcR mediates specific induction of a number of the genes of the alc cluster. This cluster includes genes involved in the oxidation of ethanol and other alcohols to acetate. The pattern of binding and of transactivation of AlcR is unique within the Zn(2)Cys(6) family. The structural bases for these specificities have not been analyzed at the atomic level until now.

RESULTS

We have used NMR spectroscopy and restrained molecular dynamics to determine a set of structures of the AlcR DNA binding domain [AlcR(1-60)] in complex with a 10-mer DNA duplex. Analysis of the structures reveals specific interactions between AlcR and DNA common to the other known zinc clusters. In addition, the involvement of the N-terminal residues upstream of the AlcR zinc cluster in DNA binding is clearly highlighted, and the pivotal role of R6 is confirmed. Totally unprecedented specific and nonspecific contacts of two additional regions of the protein with the DNA are demonstrated. The differences with the available crystallographic structures of other zinc binuclear cluster proteins-DNA complexes are analyzed.

CONCLUSIONS

The structures of the AlcR(1-60)-DNA complex provide the basis for a better understanding of some of the specificities of the AlcR system: the DNA consensus recognition sequence--usually the triplet CGG--is extended to five base pairs, AlcR acts as a monomer, and additional contacts inside and outside the DNA binding domain in the major and minor groove are observed. These extensive interactions stabilize the AlcR monomer to its cognate DNA site.

Recruitment of the transcriptional machinery through GAL11P: structure and interactions of the GAL4 dimerization domain

The GAL4 dimerization domain (GAL4-dd) is a powerful transcriptional activator when tethered to DNA in a cell bearing a mutant of the GAL11 protein, named GAL11P. GAL11P (like GAL11) is a component of the RNA-polymerase II holoenzyme. Nuclear magnetic resonance (NMR) studies of GAL4-dd revealed an elongated dimer structure with C(2) symmetry containing three helices that mediate dimerization via coiled-coil contacts. The two loops between the three coiled coils form mobile bulges causing a variation of twist angles between the helix pairs. Chemical shift perturbation analysis mapped the GAL11P-binding site to the C-terminal helix alpha3 and the loop between alpha1 and alpha2. One GAL11P monomer binds to one GAL4-dd dimer rendering the dimer asymmetric and implying an extreme negative cooperativity mechanism. Alanine-scanning mutagenesis of GAL4-dd showed that the NMR-derived GAL11P-binding face is crucial for the novel transcriptional activating function of the GAL4-dd on GAL11P interaction. The binding of GAL4 to GAL11P, although an artificial interaction, represents a unique structural motif for an activating region capable of binding to a single target to effect gene expression.

A Rsc3/Rsc30 zinc cluster dimer reveals novel roles for the chromatin remodeler RSC in gene expression and cell cycle control

Chromatin remodeling complexes perform central roles in transcriptional regulation. Here, we identify Rsc3 and Rsc30 as novel components of the essential yeast remodeler RSC complex. Rsc3 and Rsc30 function requires their zinc cluster domain, a known site-specific DNA binding motif. RSC3 is essential, and rsc3 Ts- mutants display a G2/M cell cycle arrest involving the spindle assembly checkpoint pathway, whereas rsc30Delta mutants are viable and osmosensitive. Rsc3 and Rsc30 interact functionally and also physically as a stable Rsc3/Rsc30 heteromeric complex. However, DNA microarray analysis with rsc3 or rsc30 mutants reveals different effects on the expression levels of ribosomal protein genes and cell wall genes. We propose that Rsc3 and Rsc30 interact physically but have different roles in targeting or regulating RSC.

dCtBP-dependent and -independent repression activities of the Drosophila Knirps protein

Transcriptional repressor proteins play essential roles in controlling the correct temporal and spatial patterns of gene expression in Drosophila melanogaster embryogenesis. Repressors such as Knirps, Krüppel, and Snail mediate short-range repression and interact with the dCtBP corepressor. The mechanism by which short-range repressors block transcription is not well understood; therefore, we have undertaken a detailed structure-function analysis of the Knirps protein. To provide a physiological setting for measurement of repression, the activities of endogenous or chimeric Knirps repressor proteins were assayed on integrated reporter genes in transgenic embryos. Two distinct repression functions were identified in Knirps. One repression activity depends on dCtBP binding, and this function maps to a C-terminal region of Knirps that contains a dCtBP binding motif. In addition, an N-terminal region was identified that represses in a CtBP mutant background and does not bind to the dCtBP protein in vitro. Although the dCtBP protein is important for Knirps activity on some genes, one endogenous target of the Knirps protein, the even-skipped stripe 3 enhancer, is not derepressed in a CtBP mutant. These results indicate that Knirps can utilize two different pathways to mediate transcriptional repression and suggest that the phenomenon of short-range repression may be a combination of independent activities.

Sexual dimorphism in diverse metazoans is regulated by a novel class of intertwined zinc fingers

Sex determination is regulated by diverse pathways. Although upstream signals vary, a cysteine-rich DNA-binding domain (the DM motif) is conserved within downstream transcription factors ofDrosophila melanogaster (Doublesex) and Caenorhabditis elegans (MAB-3). Vertebrate DM genes have likewise been identified and, remarkably, are associated with human sex reversal (46, XY gonadal dysgenesis). Here we demonstrate that the structure of the Doublesex domain contains a novel zinc module and disordered tail. The module consists of intertwined CCHC and HCCC Zn2+-binding sites; the tail functions as a nascent recognition α-helix. Mutations in either Zn2+-binding site or tail can lead to an intersex phenotype. The motif binds in the DNA minor groove without sharp DNA bending. These molecular features, unusual among zinc fingers and zinc modules, underlie the organization of a Drosophila enhancer that integrates sex- and tissue-specific signals. The structure provides a foundation for analysis of DM mutations affecting sexual dimorphism and courtship behavior.

Cross-pathway regulation in Saccharomyces cerevisiae: activation of the proline utilization pathway by Ga14p in vivo

The Put3p and Gal4p transcriptional activators are members of a distinct class of fungal regulators called the Cys(6) Zn(II)(2) binuclear cluster family. This family includes over 50 different Saccharomyces cerevisiae proteins that share a similar domain organization. Gal4p activates the genes of the galactose utilization pathway permitting the use of galactose as the sole source of carbon and energy. Put3p controls the expression of the proline utilization pathway that allows yeast cells to grow on proline as the sole nitrogen source. We report that Gal4p can activate the PUT structural genes in a strain lacking Put3p. We also show that the activation of PUT2 by Gal4p depends on the presence of the inducer galactose and the Put3p binding site and that activation increases with increased dosage of Gal4p. Put3p cannot activate the GAL genes in the absence of Gal4p. Our in vivo results confirm previously published in vitro data showing that Gal4p is more promiscuous than Put3p in its DNA binding ability. The results also suggest that under appropriate circumstances, Gal4p may be able to function in place of a related family member to activate expression.

NMR solution structure of AlcR (1-60) provides insight in the unusual DNA binding properties of this zinc binuclear cluster protein

The three-dimensional structure of the DNA-binding domain (residues 1-60) of the ethanol regulon transcription factor AlcR from Aspergillus nidulans has been solved by NMR. This domain belongs to the zinc binuclear cluster class. Although the core of the protein is similar to previously characterized structures, consisting of two helices organized around a Zn(2)Cys(6 )motif, the present structure presents important variations, among them the presence of two supplementary helices. This structure gives new insight into the understanding of the AlcR specificities in DNA binding such as longer consensus half-sites, in vitro monomeric binding but in vivo multiple repeat transcriptional activation, either in direct or inverse orientations. The presence of additional contacts of the protein with its DNA target can be predicted from a model proposed for the interaction with the consensus DNA target. The clustering of accessible negative charges on helix 2 delineates a possible interaction site for other determinants of the transcriptional machinery, responsible for the fine tuning of the selection of the AlcR cognate sites.

Toward ligand identification within a CCHHC zinc-binding domain from the NZF/MyT1 family

A family of proteins that contain presumed zinc-binding domains with the consensus sequence Cys-X4-CysX4-His-X7-His-X5-Cys has recently been identified, but the metal binding and structural properties of these domains have not been investigated. This consensus is striking because of the presence of five conserved potential zinc-binding residues. A peptide corresponding to the third putative zinc-binding domain from the transcription factor NZF-1 (hereafter NZF-13) has been synthesized and characterized. The UV-visible absorption spectroscopic properties of the cobalt(H) complex of this peptide demonstrate that metal binding is tetrahedral, and the position of the visible absorption bands suggests coordination by three cysteinates and one histidine. To identify which of the two conserved histidine residues acts a metal-binding residue, two histidine to alanine variant peptides were also synthesized. Both variant peptides bound cobalt(II) in a tetrahedral fashion; replacement of the first of the two histidines has a somewhat larger effect on the detailed shape of the absorption spectral features than does replacement of the second histidine. These results suggest that the metal-coordinating residues (italicized) are Cys-X4-Cys-X4-His-X7-His-Xs-Cys. However, simultaneous substitution of both histidine residues with alanine generated a peptide with much more dramatically affected metal binding properties. These observations suggests that the relatively modest effects observed for the singly substituted peptides may be due to metal interactions involving the remaining histidine. Because of these phenomena, further studies will be required to establish more conclusively the roles of the two histidine residues in metal binding and the potential significance of the apparent alternative histidine coordination.

Modulation of human heat shock factor trimerization by the linker domain

Heat shock transcription factors (HSFs) are stress-responsive proteins that activate the expression of heat shock genes and are highly conserved from bakers' yeast to humans. Under basal conditions, the human HSF1 protein is maintained as an inactive monomer through intramolecular interactions between two coiled-coil domains and interactions with heat shock proteins; upon environmental, pharmacological, or physiological stress, HSF1 is converted to a homotrimer that binds to its cognate DNA binding site with high affinity. To dissect regions of HSF1 that make important contributions to the stability of the monomer under unstressed conditions, we have used functional complementation in bakers' yeast as a facile assay system. Whereas wild-type human HSF1 is restrained as an inactive monomer in yeast that is unable to substitute for the essential yeast HSF protein, mutations in the linker region between the DNA binding domain and the first coiled-coil allow HSF1 to homotrimerize and rescue the viability defect of a hsfDelta strain. Fine mapping by functional analysis of HSF1-HSF2 chimeras and point mutagenesis revealed that a small region in the amino-terminal portion of the HSF1 linker is required for maintenance of HSF1 in the monomeric state in both yeast and in transfected human 293 cells. Although linker regions in transcription factors are known to modulate DNA binding specificity, our studies suggest that the human HSF1 linker plays no role in determining HSF1 binding preferences in vivo but is a critical determinant in regulating the HSF1 monomer-trimer equilibrium.

Major versus minor groove DNA binding of a bisarginylporphyrin hybrid molecule: a molecular mechanics investigation

On the basis of theoretical computations, we have recently synthesised [Perrée-Fauvet, M. and Gresh, N., Tetrahedron Lett., 36 (1995) 4227] a bisarginyl conjugate of a tricationic porphyrin (BAP), designed to target, in the major groove of DNA, the d(GGC GCC)2 sequence which is part of the primary binding site of the HIV-1 retrovirus site [Wain-Hobson, S. et al., Cell, 40 (1985) 9]. In the theoretical model, the chromophore intercalates at the central d(CpG)2 step and each of the arginyl arms targets O6/N7 belonging to guanine bases flanking the intercalation site. Recent IR and UV-visible spectroscopic studies have confirmed the essential features of these theoretical predictions [Mohammadi, S. et al., Biochemistry, 37 (1998) 6165]. In the present study, we compare the energies of competing intercalation modes of BAP to several double-stranded oligonucleotides, according to whether one, two or three N-methylpyridinium rings project into the major groove. Correspondingly, three minor groove binding modes were considered, the arginyl arms now targeting N3, O2 sites belonging to the purine or pyrimidine bases flanking the intercalation site. This investigation has shown that: (i) in both the major and minor grooves, the best-bound complexes have the three N-methylpyridinium rings in the groove opposite to that of the phenyl group bearing the arginyl arms; (ii) major groove binding is preferred over minor groove binding by a significant energy (29 kcal/mol); and (iii) the best-bound sequence in the major groove is d(GGC GCC)2 with two successive guanines upstream from the intercalation. On the other hand, due to the flexibility of the arginyl arms, other GC-rich sequences have close binding energies, two of them being less stable than it by less than 8 kcal/mol. These results serve as the basis for the design of derivatives of BAP with enhanced sequence selectivities in the major groove.

Probing the structure of the human Ca2+- and Zn2+-binding protein S100A3: spectroscopic investigations of its transition metal ion complexes, and three-dimensional structural model

A large-scale procedure was developed for the anaerobic purification of the human recombinant Ca2+- and Zn2+-binding protein S100A3 for spectroscopic studies. S100A3 eluted as a non-covalently bound dimer (20.8 kDa). It contained 7.5+/-0.1 free thiol groups/monomer, and bound Ca2+ with a Kd of approximately 4 mM, which corresponds to a tenfold increase in affinity compared to the aerobically purified protein. The transition metal ions Co2+, Zn2+ and Cd2+ were used as spectroscopic probes to investigate the role of the 10 cysteine residues per monomer S100A3 in metal binding. Spectrophotometric titrations suggest the formation of dinuclear thiolate-bridged clusters consisting of a Me2+(S(Cys))4 and a Me2+(S(Cys))3(N(His)) site as described for zinc finger proteins. A three-dimensional structural model of S100A3 was proposed on the basis of the NMR structure of the structurally related rabbit S100A6 protein, and taking into account the structural influence of cysteine residues.

Structural dissection of the DNA-binding domain of the yeast transcriptional activator GAL4 reveals an alpha-helical region responsible for dimerization

Limited proteolysis of the DNA-binding domain (residues 1-147) of the yeast transcriptional activator GAL4 has been used to define more precisely the subdomain structure required for DNA binding and dimerization. Two regions of the protein were found to be resistant to proteolysis: the cysteine-rich, zinc-binding region (residues 6-43) and a hydrophobic sequence between residues 52 and 97. Carboxy-terminal deletion fragments of the DNA-binding domain were generated and assayed by DNase 1 footprinting. This showed that the affinity of DNA binding depends on the sequence between residues 65 and 94. Structural comparisons by UV circular dichroism (CD) were made and the difference CD spectra indicate that strong alpha-helical content is found specifically in the region between residues 65 and 94, which previous studies have shown to enable dimerization and in this study the formation of a stable protein-DNA complex.

The use of variable density self-assembled monolayers to probe the structure of a target molecule

VP16, a protein encoded by herpes simplex virus, has a well-characterized 78 amino acid acidic activation domain. When tethered to DNA, tandem repeats of an eight amino acid motif taken from this region stimulate the transcription of a nearby gene. This work addresses how these minimal activation motifs interact with a putative target, the general transcription factor TATA box binding protein (TBP), and the biological relevance of this mechanism of action. I developed novel biophysical techniques to discriminate among three possible mechanistic models that describe how reiterated peptide motifs could synergistically effect transcription: 1) the peptide motifs simultaneously bind to quasi-identical sites on TBP, producing a high-affinity bivalent interaction that holds the general transcription factor near the start site of transcription; 2) the binding of one recognition motif causes an allosteric effect that enhances the subsequent binding of additional peptide motifs; or 3) a high-affinity interaction between the peptide repeats and TBP does occur, but rather than being the result of a "bivalent" interaction, it results from the summation of multiple interactions between the target protein and the entire length of the peptide. I generated self-assembled monolayers (SAMs) that presented different densities of the activation motif peptide in a two-dimensional array to test for avidity effects. Surface plasmon resonance (SPR) was used to measure the amount of target (TBP) binding as a function of the peptide density; a marked increase in avidity above a characteristic, critical peptide surface density was found. Competitive inhibition experiments were performed to compare the avidity of peptide motifs, tandemly repeated two or four times, and single motifs separated by a flexible linker. Four iterations of the motif, preincubated with TBP, inhibited its binding to high-density peptide surfaces approximately 250-fold better than two iterations. Single peptide motifs joined by a flexible amino acid linker inhibited TBP binding to surface peptide nearly as well as four tandem repeats. The results favor mechanistic model 1: reiterated activation motifs interact with TBP through a high-affinity interaction that is the result of the cooperative effect of single motifs simultaneously binding to separate sites on TBP. This finding is consistent with the idea that DNA-bound activation domains trigger the transcription of a nearby gene by tethering the general transcription factor, TBP, near the start site of transcription.

Zinc cluster proteins Leu3p and Uga3p recognize highly related but distinct DNA targets

Members of the family of fungal zinc cluster DNA-binding proteins possess 6 highly conserved cysteines that bind to two zinc atoms forming a structure (Zn2Cys6) that is required for recognition of specific DNA sequences. Many zinc cluster proteins have been shown to bind as homodimers to a pair of CGG triplets oriented either as direct (CGG NX CGG), inverted (CGG NX CCG), or everted repeats (CCG NX CGG), where N indicates nucleotides. Variation in the spacing between the CGG triplets also contributes to the diversity of sites recognized. For example, Leu3p binds to the everted sequence CCG N4 CGG with a strict requirement for a 4-base pair spacing. Here, we show that another member of the family, Uga3p, recognizes the same DNA motif as Leu3p. However, these transcription factors have distinct DNA targets. We demonstrate that additional specificity of binding is provided by nucleotides located between the two everted CGG triplets. Altering the 4 nucleotides between to the two everted CGG triplets switches the specificity from a Uga3p site to a Leu3p site in both in vitro and in vivo assays. Thus, our results identify a new mechanism that expands the repertoire of DNA targets of the family of zinc cluster proteins. These experiments provide a model for discrimination between targets of zinc cluster proteins.

FacB, the Aspergillus nidulans activator of acetate utilization genes, binds dissimilar DNA sequences

The facB gene is required for acetate induction of acetamidase (amdS) and the acetate utilization enzymes acetyl-CoA synthase (facA), isocitrate lyase (acuD) and malate synthase (acuE) in Aspergillus nidulans. The facB gene encodes a transcriptional activator with a GAL4-type Zn(II)2Cys6 zinc binuclear cluster DNA-binding domain which is shown to be required for DNA binding. In vitro DNA-binding sites for FacB in the 5' regions of the amdS, facA, acuD and acuE genes have been identified. Mutations in amdS FacB DNA-binding sites affected expression of an amdS-lacZ reporter in vivo and altered the affinity of in vitro DNA binding. This study shows that the FacB Zn(II)2Cys6 cluster binds to dissimilar sites which show similarity in form but not sequence with DNA-binding sites of other Zn(II)2Cys6 proteins. Sequences with homology to FacB sites are found in the 5' regions of genes regulated by the closely related yeast Zn(II)2Cys6 protein CAT8.

An electrospray ionisation mass spectrometry (ESI-MS) study to probe the metal ion binding site in the DNA binding domain of the yeast transcriptional activator GAL4

Electrospray ionisation mass spectrometry (ESI-MS) is used to detect metal ions and their stoichiometry of binding in the DNA binding domain of GAL4. In this analysis, the mass spectra of the apo- and metallo-proteins differ by both mass and charge, precluding the possibility of random adduct formation. Deuterium exchange NMR experiments of Zn(II)-GAL4(7-49) indicate that the binuclear metal ion structure, which is shown to have a net negative charge of -2, is the recipient of several hydrogen bonds, notably from the main-chain amide protons of the ligating cysteine residues, indicating the charge is stabilised in this manner.

Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster

PUT3 is a member of a family of at least 79 fungal transcription factors that contain a six-cysteine, two-zinc domain called a 'Zn2Cys6 binuclear cluster'. We have determined the crystal structure of the DNA binding region from the PUT3 protein bound to its cognate DNA target. The structure reveals that the PUT3 homodimer is bound asymmetrically to the DNA site. This asymmetry orients a beta-strand from one protein subunit into the minor groove of the DNA resulting in a partial amino acid-base pair intercalation and extensive direct and water-mediated protein interactions with the minor groove of the DNA. These interactions facilitate a sequence dependent kink at the centre of the DNA site and specify the intervening base pairs separating two DNA half-sites that are contacted in the DNA major groove. A comparison with the GAL4-DNA and PPR1-DNA complexes shows how a family of related DNA binding proteins can use a diverse set of mechanisms to discriminate between the base pairs separating conserved DNA half-sites.

Structure and mobility of the PUT3 dimer

The solution structure and backbone dynamics of the transcriptional activator PUT3 (31-100) has been characterized using NMR spectroscopy. PUT3 (31-100) contains three distinct domains: a cysteine zinc cluster, linker, and dimerization domain. The cysteine zinc cluster of PUT3 closely resembles the solution structure of GAL4, while the dimerization domain forms a long coiled-coil similar to that observed in the crystal structures of GAL4 and PPR1. However, the residues at the N-terminal end of the coiled-coil behave very differently in each of these proteins. A comparison of the structural elements within this region provides a model for the DNA binding specificity of these proteins. Furthermore, we have characterized the dynamics of PUT3 to find that the zinc cluster and dimerization domains have very diverse dynamics in solution. The dimerization domain behaves as a large protein, while the peripheral cysteine zinc clusters have dynamic properties similar to small proteins.