Zinc-dependent structure of a single-finger domain of yeast ADR1

All-Electron Calculations of the Nucleation Structures in Metal-Induced Zinc-Finger Folding: Role of the Peptide Backbone

Although the folding of individual protein domains has been extensively studied both experimentally and theoretically, protein folding induced by a metal cation has been relatively understudied. Almost all folding mechanisms emphasize the role of the side-chain interactions rather than the peptide backbone in the protein folding process. Herein, we focus on the thermodynamics of the coupled metal binding and protein folding of a classical zinc-finger (ZF) peptide, using all-electron calculations to obtain the structures of possible nucleation centers and free energy calculations to determine their relative stability in aqueous solution. The calculations indicate that a neutral Cys first binds to hexahydrated Zn2+ via its ionized sulfhydryl group and neutral backbone oxygen, with the release of four water molecules and a proton. Another nearby Cys then binds in the same manner as the first one, yielding a fully dehydrated Zn2+. Subsequently, two His ligands from the C-terminal part of the peptide successively dislodge the Zn-bound backbone oxygen atoms to form the native-like Zn-(Cys)2(His)2 complex. Each successive Zn complex accumulates increasingly favorable and native interactions, lowering the energy of the ZF polypeptide, which concomitantly becomes more compact, reducing the search volume, thus guiding folding to the native state. In the protein folding process, not only the side chains but also the backbone peptide groups play a critical role in stabilizing the nucleation structures and promoting the hydrophobic core formation.

Zinc fingers 1 and 7 of yeast TFIIIA are essential for assembly of a functional transcription complex on the 5 S RNA gene

The binding of transcription factor (TF) IIIA to the internal control region of the 5 S RNA gene is the first step in the assembly of a DNA–TFIIIA–TFIIIC– TFIIIB transcription complex, which promotes accurate transcription by RNA polymerase III. With the use of mutations that are predicted to disrupt the folding of a zinc finger, we have examined the roles of zinc fingers 1 through 7 of yeast TFIIIA in the establishment of a functional transcription complex both in vitro and in vivo. Our data indicate that, in addition to their role in DNA binding, the first and seventh zinc fingers contribute other essential roles in the assembly of an active transcription complex. Alanine-scanning mutagenesis identified residues within zinc finger 1 that are not required for DNA binding but are required for incorporation of TFIIIC into the TFIIIA–DNA complex. Although disruption of zinc finger 2 or 3 had a deleterious effect on the activity of TFIIIA both in vitro and in vivo, we found that increasing the level of their in vivo expression allowed these mutant proteins to support cell viability. Disruption of zinc fingers 4, 5 or 6 had minimal effect on the DNA binding and TF activities of TFIIIA.

Investigations of Metal-Coordinated Peptides as Supramolecular Synthons

This article describes the synthesis and controlled assembly of four model biological-hybrid scaffolds via coordination of a metal complex to four new tripeptides. Each model tripeptide investigated has either a central pyridyl glycyl or a pyridyl alanyl residue between two terminally protected glycines. All tripeptides were coordinated to their complementary recognition unit, a p-methoxy SCS-Pd pincer complex. The assembly events were fully characterized and investigated by 1H NMR, ES-MS, and isothermal titration calorimetry (ITC) to elucidate how the substitution and spatial distance of the pyridyl moiety to the peptide backbone affects the metal coordination. Using these characterization techniques, we have shown that the metal-coordination events in all cases are fast and quantitative and that the peptide backbones do not interfere with the self-assembly. The ITC analyses showed that the 4-pyridyl tripeptides are the tightest binding ligands toward the palladated pincer complexes with the alanyl derivative being the strongest overall, demonstrating the superiority of the 4-pyridyl peptides over their 3-pyridyl analogues. The measured association constants are comparable to other pincer-pyridine systems in DMSO suggesting that the controlled coordination of the metalated pincer/pyridine interaction is an interesting biological synthon and will allow for the future development of important noncovalent peptide-based hybrid materials.

Glucose signaling in Saccharomyces cerevisiae

Eukaryotic cells possess an exquisitely interwoven and fine-tuned series of signal transduction mechanisms with which to sense and respond to the ubiquitous fermentable carbon source glucose. The budding yeast Saccharomyces cerevisiae has proven to be a fertile model system with which to identify glucose signaling factors, determine the relevant functional and physical interrelationships, and characterize the corresponding metabolic, transcriptomic, and proteomic readouts. The early events in glucose signaling appear to require both extracellular sensing by transmembrane proteins and intracellular sensing by G proteins. Intermediate steps involve cAMP-dependent stimulation of protein kinase A (PKA) as well as one or more redundant PKA-independent pathways. The final steps are mediated by a relatively small collection of transcriptional regulators that collaborate closely to maximize the cellular rates of energy generation and growth. Understanding the nuclear events in this process may necessitate the further elaboration of a new model for eukaryotic gene regulation, called "reverse recruitment." An essential feature of this idea is that fine-structure mapping of nuclear architecture will be required to understand the reception of regulatory signals that emanate from the plasma membrane and cytoplasm. Completion of this task should result in a much improved understanding of eukaryotic growth, differentiation, and carcinogenesis.

REM1, a new type of long terminal repeat retrotransposon in Chlamydomonas reinhardtii

A new long terminal repeat (LTR) retrotransposon, named REM1, has been identified in the green alga Chlamydomonas reinhardtii. It was found in low copy number, highly methylated, and with an inducible transpositional activity. This retrotransposon is phylogenetically related to Ty3-gypsy LTR retrotransposons and possesses new and unusual structural features. A regulatory module, ORF3p, is present in an inverse transcriptional orientation to that of the polyprotein and contains PHD-finger and chromodomains, which might confer specificity of the target site and are highly conserved in proteins involved in transcriptional regulation by chromatin remodeling. By using different wild-type and mutant strains, we show that CrREM1 was active with a strong transcriptional activity and amplified its copy number in strains that underwent foreign DNA integration and/or genetic crosses. However, integration of CrREM1 was restricted to these events even though the expression of its full-length transcripts remained highly activated. A regulatory mechanism of CrREM1 retrotransposition which would help to minimize its deleterious effects in the host genome is proposed.

Calcium Ion Responsive DNA Binding in a Zinc Finger Fusion Protein

Zinc finger fusion proteins, having a Ca-binding site from troponin C, were created to develop Ca-responsive regulation of DNA binding. The typical zinc finger folding of a novel fusion protein with a single finger, F2-Tn, was investigated using UV-vis spectroscopy of the Co-substituted form and CD experiments. Detailed structural analyses of F2-Tn/Zn2+ using NMR experiments and structural calculations clarify that our fusion protein gives a native zinc finger folding with the artificial Ca-binding domain intervening two helices. The Ca-responsive DNA-binding affinity of troponin-fused protein with two fingers (using F1F2-Tn) was investigated by electrophoretic mobility shift assay (EMSA). EMSA analyses of F1F2-Tn were performed under the conditions of various concentrations of the Ca ion. F1F2-Tn has a Kd value of 5.8 nM in the absence of Ca ion and shows a higher Kd value of 13 nM in the presence of 100 equiv of Ca ion. The artificially designed fusion zinc finger protein with a Ca-binding domain has Ca-responsive DNA-binding affinity. It is leading to a better understanding of the construction of zinc finger-based artificial transcriptional factors with a Ca switch.

Zn-, Cd-, and Pb-transcription factor IIIA: properties, DNA binding, and comparison with TFIIIA-finger 3 metal complexes

Properties of the metal ion binding sites of Zn-transcription factor IIIA (TFIIIA) were investigated to understand the potential of this type of zinc finger to undergo reactions that remove Zn(2+) from the protein. Zn-TFIIIA was purified from E. coli containing the cloned sequence for Xenopus laevis oocyte TFIIIA and its stoichiometry of bound Zn(2+) was shown to depend on the details of the isolation process. The average dissociation constant of Zn(2+) in Zn-TFIIIIA was 10(-7). The dissociation constant for Zn-F3, the third finger from the N-terminus of TFIIIA, was 1.0 x 10(-8). The reactivity of Zn-TFIIIA with a series of metal binding ligands, including 2-carboxy-2'-hydroxy-5'-sulfoformazylbenzene (zincon), 4-(2-pyridylazo)-resorcinol (PAR), and 3-ethoxy-2-oxo-butyraldehyde-bis-(N(4)-dimethylthiosemicarbazone) (H(2)KTSM(2)) revealed similar kinetics. The reactivity of PAR with Zn-TFIIIA declined substantially when the protein was bound to the internal control region (ICR) of the 5S ribosomal DNA. Both Cd(2+) and Pb(2+) disrupt TFIIIA binding to its cognate DNA sequence. The Pb(2+) dissociation constant of Pb-F3 was measured as 2.5 x 10(-8). According to NMR spectroscopy, F3 does not fold into a regular conformation in the presence of Pb(2+).

Modulation of zinc- and cobalt-binding affinities through changes in the stability of the zinc ribbon protein L36

Cysteine-rich Zn(II)-binding sites in proteins serve two distinct functions: to template or stabilize specific protein folds, and to facilitate chemical reactions such as alkyl transfers. We are interested how the protein environment controls metal site properties, specifically, how naturally occurring tetrahedral Zn(II) sites are affected by the surrounding protein. We have studied the Co(II)- and Zn(II)-binding of a series of derivatives of L36, a small zinc ribbon protein containing a (Cys)(3)His metal coordination site. UV-vis spectroscopy was used to monitor metal binding by peptides at pH 6.0. For all derivatives, the following trends were observed: (1) Zn(II) binds tighter than Co(II), with an average K (A) (Zn) /K (A) (Co) of 2.8(+/-2.0)x10(3); (2) mutation of the metal-binding ligand His32 to Cys decreases the affinity of L36 derivatives for both metals; (3) a Tyr24 to Trp mutation in the beta-sheet hydrophobic cluster increases K (A) (Zn) and K (A) (Co) ; (4) mutation in the beta-hairpin turn, His20 to Asn generating an Asn-Gly turn, also increases K (A) (Zn) and K (A) (Co) ; (5) the combination of His20 to Asn and Tyr24 to Trp mutations also increases K (A) (Zn) and K (A) (Co) , but the increments versus C(3)H are less than those of the single mutations. Furthermore, circular dichroism, size-exclusion chromatography, and 1D and 2D (1)H NMR experiments show that the mutations do not change the overall fold or association state of the proteins. L36, displaying Co(II)- and Zn(II)-binding sensitivity to various sequence mutations without undergoing a change in protein structure, can therefore serve as a useful model system for future structure/reactivity studies.

Gene Regulation in Spermatogenesis

Mammalian spermatogenesis is a complex hormone-dependent developmental program in which a myriad of events must take place to ensure that germ cells reach their proper stage of development at the proper time. Many of these events are controlled by cell type- and stage-specific transcription factors. The regulatory mechanisms involved provide an intriguing paradigm for the field of developmental biology and may lead to the development of new contraceptives an and innovative routs to treat male infertility. In this review, we address three aspects of the genetic regulatory mechanism that drive spermatogenesis. First, we detail what is known about how steroid hormones (both androgens and estrogens) and their cognate receptors initiate and maintain mammalian spermatogenesis. Steroids act through three mechanistic routes: (i) direct activation of genes through hormone-dependent promoter elements, (ii) secondary transcriptional responses through activation of hormone-dependent transcription factors, and (iii) rapid, transcription-independent (nonclassical) events induced by steroid hormones. Second, we provide a survey of transcription factors that function in mammalian spermatogenesis, including homeobox, zinc-finger, heat-shock, and cAMP-response family members. Our survey is not intended to cover all examples but to give a flavor for the gamut of biological roles conferred by transcription factors in the testis, particularly those defined in knockout mice. Third, we address how testis-specific transcription is achieved. In particular, we cover the evidence for and against the idea that some testis-specific genes are transcriptionally silent in somatic tissues as a result of DNA methylation.

Interprotein metal exchange between transcription factor IIIa and apo-metallothionein

Zn(2+) and Cd(2+) ion exchange between transcription factor IIIA (TFIIIA) and apo-metallothionein (MT) were studied using a combination of methods including chromatography, ultrafiltration and UV spectroscopy. Under near stoichiometric conditions, apoMT was able to remove most if not all of the zinc ions from TFIIIA, whether or not the TFIIIA was bound to the 5S DNA internal control region (ICR), and concomitantly inhibit its DNA-binding activity as indicated by an electrophoretic mobility shift assay. The kinetics of the two processes were similar. The rate of the metal exchange reaction increased with the concentrations of both reactants. A second-order rate constant of 30+/-10 M(-1)s(-1) was calculated. Similar observations were made for the reaction between apoMT and Cd-substituted TFIIIA, which proceeded without observable intermediates according to a spectrophotometric analysis. A very slow metal ion exchange occurred between Cd-TFIIIA and Zn-MT, but not between Cd-MT and Zn-TFIIIA. Comparative studies on the reaction of TFIIIA with a small competing ligand, ethylenedinitrilo-tetraacetic acid (EDTA), were also conducted. Although EDTA reacts with free Zn-TFIIIA, under similar conditions it failed to compete for Zn(2+) bound as Zn-TFIIIA-ICR.

Saccharomyces cerevisiae Hop1 zinc finger motif is the minimal region required for its function in vitro

Saccharomyces cerevisiae meiosis-specific HOP1, which encodes a core component of synaptonemal complex, plays a key role in proper pairing of homologous chromosomes and processing of meiotic DNA double strand breaks. Isolation and analysis of hop1 mutants indicated that these functions require Cys(371) of Hop1 embedded in a region (residues 343-378) sharing homology to a zinc finger motif (ZnF). However, the precise biochemical function of Hop1, or its putative ZnF, in these processes is poorly understood. Our previous studies revealed that Hop1 is a DNA-binding protein, showed substantially higher binding affinity for G4 DNA, and enhances its formation. We report herein that ZnF appears to be sufficient for both zinc as well as DNA-binding activities. Molecular modeling studies suggested that Hop1 ZnF differs from the previously characterized natural ZnFs. The zinc-binding assay showed that the affinity for zinc is weaker for C371S ZnF mutant compared with the wild type (WT) ZnF. Analysis of CD spectra indicated that zinc and DNA induce substantial conformational changes in WT ZnF, but not in C371S ZnF mutant. The results from a number of different experimental approaches suggested that the DNA-binding properties of ZnF are similar to those of full-length Hop1 and that interaction with DNA rich in G residues is particularly robust. Significantly, WT ZnF by itself, but not C371S mutant, was able to bind duplex DNA and promote interstitial pairing of DNA double helices via the formation of guanine quartets. Together, these results implicate a direct role for Hop1 in pairing of homologous chromosomes during meiosis.

The maize ID1 flowering time regulator is a zinc finger protein with novel DNA binding properties

The INDETERMINATE protein, ID1, plays a key role in regulating the transition to flowering in maize. ID1 is the founding member of a plant-specific zinc finger protein family that is defined by a highly conserved amino sequence called the ID domain. The ID domain includes a cluster of three different types of zinc fingers separated from a fourth C2H2 finger by a long spacer; ID1 is distinct from other ID domain proteins by having a much longer spacer. In vitro DNA selection and amplification binding assays and DNA binding experiments showed that ID1 binds selectively to an 11 bp consensus motif via the ID domain. Unexpectedly, site-directed mutagenesis of the ID1 protein showed that zinc fingers located at each end of the ID domain are not required for binding to the consensus motif despite the fact that one of these zinc fingers is a canonical C2H2 DNA binding domain. In addition, an ID1 in vitro deletion mutant that lacks the extra spacer between zinc fingers binds the same 11 bp motif as normal ID1, suggesting that all ID domain-containing proteins recognize the same DNA target sequence. Our results demonstrate that maize ID1 and ID domain proteins have novel zinc finger configurations with unique DNA binding properties.

A novel cysteine cluster in human metal-responsive transcription factor 1 is required for heavy metal-induced transcriptional activation in vivo

Metal-responsive transcription factor 1 (MTF-1) specifically binds to metal response elements (MREs) associated with a number of metal- and stress-responsive genes. Human MTF-1 contains a cysteine-rich cluster, -632Cys-Gln-Cys-Gln-Cys-Ala-Cys638-, conserved from pufferfish to humans far removed from the MRE-binding zinc finger domain and just C-terminal to a previously mapped serine/threonine-rich transcriptional activation domain. MTF-1 proteins containing two Cys-->Ala substitutions (C632A/C634A) or a deletion in this region altogether (Delta(632-644)) are significantly impaired in their ability to induce Zn(II)- and Cd(II)-responsive transcription of a MRE-linked reporter gene in transiently transfected mouse dko7 (MTF-1-/-) cells in culture under moderate metal stress but retain the ability to drive basal levels of transcription in a MRE-dependent manner in vivo and in vitro. In addition, the mutated proteins respond to induction by Zn(II) or Cd(II) with nuclear translocation and MRE binding activities comparable with wild-type MTF-1. Attempts to rescue the Delta(632-644) deletion mutant phenotype by inserting similar Cys-rich sequences from Drosophila MTF-1 were unsuccessful, suggesting that the structure of this motif within intact human MTF-1, rather than the simple presence of multiple closely spaced Cys residues, is required for function. This cysteine cluster therefore functions at a step subsequent to nuclear translocation and MRE-binding DNA to naked promoter-containing DNA and appears to be specifically required for MTF-1 to activate transcription in the presence of inducing heavy metal ions.

KRAB zinc finger proteins: an analysis of the molecular mechanisms governing their increase in numbers and complexity during evolution

Krüppel-related zinc finger proteins, with 564 members in the human genome, probably constitute the largest individual family of transcription factors in mammals. Approximately 30% of these proteins carry a potent repressor domain called the Krüppel associated box (KRAB). Depending on the structure of the KRAB domain, these proteins have been further divided into three subfamilies (A + B, A + b, and A only). In addition, some KRAB zinc finger proteins contain another conserved motif called SCAN. To study their molecular evolution, an extensive comparative analysis of a large panel of KRAB zinc finger genes was performed. The results show that both the KRAB A + b and the KRAB A subfamilies have their origin in a single member or a few closely related members of the KRAB A + B family. The KRAB A + B family is also the most prevalent among the KRAB zinc finger genes. Furthermore, we show that internal duplications of individual zinc finger motifs or blocks of several zinc finger motifs have occurred quite frequently within this gene family. However, zinc finger motifs are also frequently lost from the open reading frame, either by functional inactivation by point mutations or by the introduction of a stop codon. The introduction of a stop codon causes the exclusion of part of the zinc finger region from the coding region and the formation of graveyards of degenerate zinc finger motifs in the 3'-untranslated region of these genes. Earlier reports have shown that duplications of zinc finger genes commonly occur throughout evolution. We show that there is a relatively low degree of sequence conservation of the zinc finger motifs after these duplications. In many cases this may cause altered binding specificities of the transcription factors encoded by these genes. The repetitive nature of the zinc finger region and the structural flexibility within the zinc finger motif make these proteins highly adaptable. These factors may have been of major importance for their massive expansion in both number and complexity during metazoan evolution.

Contribution of individual zinc ligands to metal binding and peptide folding of zinc finger peptides

Little is known about the contribution of individual zinc-ligating amino acid residues for coupling between zinc binding and protein folding in zinc finger domains. To understand such roles of each zinc ligand, four zinc finger mutant peptides corresponding to the second zinc finger domain of Sp1 were synthesized. In the mutant peptides, glycine was substituted for one of four zinc ligands. Their metal binding and folding properties were spectroscopically characterized and compared to those of the native zinc finger peptide. In particular, the electronic charge-transfer and d-d bands of the Co(II)-substituted peptide complexes were used to examine the metal coordination number and geometry. Fluorescence emission studies revealed that the mutant peptides are capable of binding zinc despite removing one ligand. Circular dichroism results clearly showed the induction of an alpha-helix by zinc binding. In addition, the structures of certain mutant zinc finger peptides were simulated by molecular dynamics calculation. The information indicates that His23 and the hydrophobic core formed between the alpha-helix and the beta-sheet play an essential role in alpha-helix induction. This report demonstrates that each ligand does not contribute equally to alpha-helix formation and coordination geometry in the zinc finger peptide.

Novel strategy for the design of a new zinc finger: creation of a zinc finger for the AT-rich sequence by alpha-helix substitution

In this communication, a novel strategy for the design of a zinc finger peptide on the basis of alpha-helix substitution has been demonstrated. Sp1HM is a helix-substituted mutant for the wild-type Sp1(zf123) and its alpha-helix of each finger is replaced by that of fingers 4-6 of CF2-II. The circular dichroism spectrum of Sp1HM suggests that Sp1HM has an ordered secondary structure similar to that of Sp1(zf123). From the analyses of the DNA binding affinity and specificity by gel mobility shift assay, it is clearly indicated that Sp1HM specifically binds to the AT-rich sequence (5'-GTA TAT ATA-3') with 3.2 nM dissociation constants. Moreover, the zinc finger peptides for the sequence alternating between the AT- and GC-rich subsites can also be created by the alpha-helix substitution. This strategy is evidently effective and is also more convenient than the phage display method. Consequently, our design method is widely applicable to creating zinc finger peptides with novel binding specificities.

Metal-dependent folding and stability of nuclear hormone receptor DNA-binding domains

The nuclear/hormone receptors are an extensive family of ligand-activated transcription factors that recognise DNA targets through a highly conserved, structurally autonomous DNA-binding domain. The compact structure of the DNA-binding domain is supported by two zinc ions, each of which is co-ordinated by the tetrahedral arrangement of thiol groups from four cysteine residues. Metal binding is expected to be linked with deprotonation of the co-ordinating thiol groups and folding of the polypeptide. Using a variety of biophysical approaches, we characterise these linked equilibria for the isolated DNA-binding domains (DBD) of the receptors for estrogen and glucocorticoid. Mass spectrometry and equilibrium denaturation indicate that, near neutral pH, approximately four of the eight co-ordinating thiol groups release protons with zinc uptake, in agreement with the expected pK(a) change for the -SH group in the presence of the metal. Mass spectrometry reveals that the protein charge distribution changes with the uptake of zinc and that metal binding is co-operative. The co-operativity is consistent with observations from equilibrium denaturation, which indicate that the folding event is a two-state process. A crucial residue that stabilises the equilibrium structure of the DBD fold itself is a cysteine residue situated in the hydrophobic core of all known nuclear hormone receptors (but not involved in metal binding): it appears to be conserved absolutely for its unique combination of size and hydrophobicity. Stabilisation of the DBDs could be achieved by truncating the flexible, basic termini, suggesting that like-charge clusters may have deleterious effects on protein folds. While the metal-free apo protein and the chemically denatured state have little defined secondary structure, these states were expanded only partially in comparison with the native structure, according to data from small-angle X-ray scattering. The comparatively compact shapes of the denatured and apo forms may explain, in part, the marginal stability of the native fold.

Zinc is required for structural stability of the C-terminus of archaeal translation initiation factor aIF2beta

aIF2beta is an archaeal homolog of eukaryotic translation factor eIF2beta necessary for translation initiation and involved in recognition of the initiation codon. In the present study, we demonstrate for the first time zinc binding to the C2-C2 zinc finger at the C-terminus of aIF2beta. Nuclear magnetic resonance backbone assignments were also determined and the secondary structural elements identified.

The hidden thermodynamics of a zinc finger

The Zn finger provides a model for studies of protein structure and stability. Its core contains a conserved phenylalanine residue adjoining three architectural elements: a beta-hairpin, an alpha-helix and a tetrahedral Zn(2+)-binding site. Here, we demonstrate that the consensus Phe is not required for high-affinity Zn(2+) binding but contributes to the specification of a precise DNA-binding surface. Substitution of Phe by leucine in a ZFY peptide permits Zn(2+)-dependent folding. Although a native-like structure is retained, structural fluctuations lead to attenuation of selected nuclear Overhauser enhancements and accelerated amide proton exchange. Surprisingly, wild-type Zn affinity is maintained by entropy-enthalpy compensation (EEC): a hidden entropy penalty (TDeltaDeltaS 7kcal/mol) is balanced by enhanced enthalpy of association (DeltaDeltaH -7kcal/mol) at 25 degrees C. Because the variant is less well ordered than the Phe-anchored domain, the net change in entropy is opposite to the apparent change in configurational entropy. By analogy to the thermodynamics of organometallic complexation, we propose that EEC arises from differences in solvent reorganization. Exclusion of Leu among biological sequences suggests an evolutionary constraint on the dynamics of a Zn finger.

Conformational heterogeneity in the C-terminal zinc fingers of human MTF-1: an NMR and zinc-binding study

The human metalloregulatory transcription factor, metal-response element (MRE)-binding transcription factor-1 (MTF-1), contains six TFIIIA-type Cys(2)-His(2) motifs, each of which was projected to form well-structured betabetaalpha domains upon Zn(II) binding. In this report, the structure and backbone dynamics of a fragment containing the unusual C-terminal fingers F4-F6 has been investigated. (15)N heteronuclear single quantum coherence (HSQC) spectra of uniformly (15)N-labeled hMTF-zf46 show that Zn(II) induces the folding of hMTF-zf46. Analysis of the secondary structure of Zn(3) hMTF-zf46 determined by (13)Calpha chemical shift indexing and the magnitude of (3)J(Halpha-HN) clearly reveal that zinc fingers F4 and F6 adopt typical betabetaalpha structures. An analysis of the heteronuclear backbone (15)N relaxation dynamics behavior is consistent with this picture and further reveals independent tumbling of the finger domains in solution. Titration of apo-MTF-zf46 with Zn(II) reveals that the F4 domain binds Zn(II) significantly more tightly than do the other two finger domains. In contrast to fingers F4 and F6, the betabetaalpha fold of finger F5 is unstable and only partially populated at substoichiometric Zn(II); a slight molar excess of zinc results in severe conformational exchange broadening of all F5 NH cross-peaks. Finally, although Cd(II) binds to apo-hMTF-zf46 as revealed by intense S(-)-->Cd(II) absorption, a non-native structure results; addition of stoichiometric Zn(II) to the Cd(II) complex results in quantitative refolding of the betabetaalpha structure in F4 and F6. The functional implications of these results are discussed.

Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs

With the complete human genomic sequence being unraveled, the focus will shift to gene identification and to the functional analysis of gene products. The generation of a set of cDNAs, both sequences and physical clones, which contains the complete and noninterrupted protein coding regions of all human genes will provide the indispensable tools for the systematic and comprehensive analysis of protein function to eventually understand the molecular basis of man. Here we report the sequencing and analysis of 500 novel human cDNAs containing the complete protein coding frame. Assignment to functional categories was possible for 52% (259) of the encoded proteins, the remaining fraction having no similarities with known proteins. By aligning the cDNA sequences with the sequences of the finished chromosomes 21 and 22 we identified a number of genes that either had been completely missed in the analysis of the genomic sequences or had been wrongly predicted. Three of these genes appear to be present in several copies. We conclude that full-length cDNA sequencing continues to be crucial also for the accurate identification of genes. The set of 500 novel cDNAs, and another 1000 full-coding cDNAs of known transcripts we have identified, adds up to cDNA representations covering 2%--5 % of all human genes. We thus substantially contribute to the generation of a gene catalog, consisting of both full-coding cDNA sequences and clones, which should be made freely available and will become an invaluable tool for detailed functional studies.

NMR identification of heavy metal-binding sites in a synthetic zinc finger peptide: toxicological implications for the interactions of xenobiotic metals with zinc finger proteins

Lead (Pb), mercury (Hg), and cadmium (Cd) are toxic and interfere with protein metal-binding sites. The Cys(2)/His(2) zinc finger is a structural motif required for sequence-specific DNA binding and is present in zinc finger transcription factors (ZFP): Sp1, Egr-1, and TFIIIA. Neurotoxic studies have shown that heavy metals directly inhibit the DNA binding of ZFP and result in adverse cellular effects. Recently, we demonstrated the ability of heavy metals to alter the DNA binding of a synthetic Cys(2)/His(2) finger peptide (Razmiafshari and Zawia, Toxicol. Appl. Pharmacol. 166, 1-12, 2000). To determine the precise site of interactions between heavy metals and this protein domain, Pb, Hg, Cd, and Ca were reconstituted with the synthetic apopeptide and studied by one- and two-dimensional NMR spectroscopy. In the presence of Zn, Cd, Hg, and Pb, but not Ca, distinct peptide NMR signal changes in the aliphatic region were observed and attributed to metal-cystiene interactions. However, chemical shifts indicative of metal-histidine binding were elicited by all the metals in the peptide's aromatic region. Chemical shift assignments and sequential connectivity were established in the presence and absence of Zn, Pb, and Ca through TOCSY and NOESY spectra. Cysteine and histidine residues showed a distinct change in their amide and beta resonances in the presence of Zn and Pb, suggesting the metal-ligand binding sites were near these residues. However, Ca led to no significant spectral changes in these regions, suggesting that it is not actively involved in the binding site. These studies reveal this structure as a mediator of metal-induced alterations in protein function.

DNA recognition by Cys2His2 zinc finger proteins

Cys2His2 zinc fingers are one of the most common DNA-binding motifs found in eukaryotic transcription factors. These proteins typically contain several fingers that make tandem contacts along the DNA. Each finger has a conserved beta beta alpha structure, and amino acids on the surface of the alpha-helix contact bases in the major groove. This simple, modular structure of zinc finger proteins, and the wide variety of DNA sequences they can recognize, make them an attractive framework for attempts to design novel DNA-binding proteins. Several studies have selected fingers with new specificities, and there clearly are recurring patterns in the observed side chain-base interactions. However, the structural details of recognition are intricate enough that there are no general rules (a "recognition code") that would allow the design of an optimal protein for any desired target site. Construction of multifinger proteins is also complicated by interactions between neighboring fingers and the effect of the intervening linker. This review analyzes DNA recognition by Cys2His2 zinc fingers and summarizes progress in generating proteins with novel specificities from fingers selected by phage display.

The metal binding properties of the CCCH motif of the 50S ribosomal protein L36 from Thermus thermophilus

The TthL36 protein of the 50S ribosomal proteins from Thermus thermophilus has been found to contain the rare C(Xaa)2C(Xaa)12C(Xaa)4H (CCCH) sequence motif, a zinc finger binding motif, which for other zinc finger proteins is known to cleave RNA hairpins. In order to investigate the metal-binding properties of this T. thermophilus TthL36 protein, the core 26-mer polypeptide containing this CCCH motif was prepared by solid-phase peptide synthesis methods using Fmoc chemistry, purified by preparative RP-HPLC and characterized by circular dichroism, high-performance capillary zone electrophoresis and electrospray ionization mass spectrometry. Reaction of the acetamidomethyl (Acm)-protected polypeptide with iodine under acidic conditions resulted in the formation of the fully de-protected polypeptide. Of interest, the results demonstrate that the standard Acm-deprotection method with the synthetic TthL36 polypeptide using mercuric acetate in the presence of a large excess of 2-mercaptoethanol resulted in preferential formation of a very stable mercuro-polypeptide complex. The properties of the Acm-deprotected polypeptide in the presence of different metal ions were also investigated by spectroscopic methods. The results confirm that this TthL36 polypeptide containing the CCCH motif binds metal ions with different affinities, namely in the order Co(II)>Hg(II)>Zn(II).

The third zinc finger of TFIIIA stabilizes a hairpin structure of the non-coding strand in the internal control region of 5S RNA gene

The structures of non-coding and coding strands in box C of the internal control region (ICR) of Xenopus laevis somatic 5S RNA gene have been examined by circular dichroism (CD) and Raman spectroscopy in the absence and presence of the third zinc finger of transcription factor IIIA (TFIIIA), which binds to the ICR. The non-coding strand exhibits CD signals assignable to a hairpin and an unfolded structure. The presence of the hairpin structure is supported by Raman spectra, gel electrophoresis, and nucleotide deletion experiments. Binding of the zinc finger to the non-coding strand increases the CD signal of hairpin structure, indicating stabilization of the hairpin structure by the zinc finger. In contrast, the corresponding coding strand remains unfolded even in the presence of the zinc finger. The TFIIIA-ICR complex is not only required for initiation of transcription but also lasts during many rounds of transcription of the 5S RNA gene including the ICR (Bogenhagen et al., Cell 28 (1982) 413). TFIIIA may play a role in promoting the transcription by maintaining the unwound non-coding strand in the hairpin structure and leaving the coding strand available for transcription by RNA polymerase.

Design strategies for the construction of independently folded polypeptide motifs

In this paper we present a redesign strategy for the development of uniquely folded polypeptide motifs of less than 40 residues. These mini proteins are based on natural target domains, including the zinc finger domains (BBA motif)* and the disulfide-rich snake and scorpion toxins (BBB motif). These motifs are designed to act as the molecular framework for the construction of novel functional polypeptides. We will explore the structural determinants of the folded BBA motif, inspired by the zinc finger peptides, in relation to the redesign process.

brakeless is required for lamina targeting of R1-R6 axons in the Drosophila visual system

Photoreceptors in the Drosophila eye project their axons retinotopically to targets in the optic lobe of the brain. The axons of photoreceptor cells R1-R6 terminate in the first optic ganglion, the lamina, while R7 and R8 axons project through the lamina to terminate in distinct layers of the second ganglion, the medulla. Here we report the identification of the gene brakeless (bks) and show that its function is required in the developing eye specifically for the lamina targeting of R1-R6 axons. In mosaic animals lacking bks function in the eye, R1-R6 axons project through the lamina to terminate in the medulla. Other aspects of visual system development appear completely normal: photoreceptor and lamina cell fates are correctly specified, R7 axons correctly target the medulla, and both correctly targeted R7 axons and mistargeted R1-R6 axons maintain their retinotopic order with respect to both anteroposterior and dorsoventral axes. bks encodes two unusually hydrophilic nuclear protein isoforms, one of which contains a putative C(2)H(2) zinc finger domain. Transgenic expression of either Bks isoform is sufficient to restore the lamina targeting of R1-R6 axons in bks mosaics, but not to retarget R7 or R8 axons to the lamina. These data demonstrate the existence of a lamina-specific targeting mechanism for R1-R6 axons in the Drosophila visual system, and provide the first entry point in the molecular characterization of this process.

Structural organization of Staf-DNA complexes

The transactivator Staf, which contains seven contiguous zinc fingers of the C(2)-H(2)type, exerts its effects on gene expression by binding to specific targets in vertebrate small nuclear RNA (snRNA) and snRNA-type gene promoters. Here, we have investigated the interaction of the Staf zinc finger domain with the optimal Xenopus selenocysteine tRNA (xtRNA(Sec)) and human U6 snRNA (hU6) Staf motifs. Generation of a series of polypeptides containing increasing numbers of Staf zinc fingers tested in binding assays, by interference techniques and by binding site selection served to elucidate the mode of interaction between the zinc fingers and the Staf motifs. Our results provide strong evidence that zinc fingers 3-6 represent the minimal zinc finger region for high affinity binding to Staf motifs. Furthermore, we show that the binding of Staf is achieved through a broad spectrum of close contacts between zinc fingers 1-6 and xtRNA(Sec)or optimal sites or between zinc fingers 3-6 and the hU6 site. Extensive DNA major groove contacts contribute to the interaction with Staf that associates more closely with the non-template than with the template strand. Based on these findings and the structural information provided by the solved structures of other zinc finger-DNA complexes, we propose a model for the interaction between Staf zinc fingers and the xtRNA(Sec), optimal and hU6 sites.

Interaction of a novel cysteine and histidine-rich cytoplasmic protein with galectin-3 in a carbohydrate-independent manner

We have used the yeast two-hybrid system to search for cytoplasmic proteins that might assist in the intracellular trafficking of the soluble beta-galactoside-binding protein, galectin-3. We utilised as bait murine full-length galectin-3 to screen a murine 3T3 cDNA library. Several interacting clones were found to encode a partial open reading frame and a full-length clone was obtained by rapid amplification of cDNA ends methodology. In various assays in vitro the novel protein was shown to bind galectin-3 in a carbohydrate-independent manner. The novel protein contains an unusually high content of cysteine and histidine residues and shows significant sequence homologies with several metal ion-binding motifs present in known proteins. Confocal immunofluorescence microscopy of permeabilised 3T3 cells shows a prominent perinuclear, as well as cytoplasmic, localisation of the novel protein.

DNA-induced alpha-helix capping in conserved linker sequences is a determinant of binding affinity in Cys(2)-His(2) zinc fingers

High-affinity, sequence-specific DNA binding by Cys(2)-His(2) zinc finger proteins is mediated by both specific protein-base interactions and non-specific contacts between charged side-chains and the phosphate backbone. In addition, in DNA complexes of multiple zinc fingers, protein-protein interactions between the finger units contribute to the binding affinity. We present NMR evidence for another contribution to high- affinity binding, a highly specific DNA-induced helix capping involving residues in the linker sequence between fingers. Capping at the C terminus of the alpha-helix in each zinc finger, incorporating a consensus TGEKP linker sequence that follows each finger, provides substantial binding energy to the DNA complexes of zinc fingers 1-3 of TFIIIA (zf1-3) and the four zinc fingers of the Wilms' tumor suppressor protein (wt1-4). The same alpha-helix C-capping motif is observed in the X-ray structures of four other protein-DNA complexes. The structures of each of the TGEKP linkers in these complexes can be superimposed on the linker sequences in the zf1-3 complex, revealing a remarkable similarity in both backbone and side-chain conformations. The canonical linker structures from the zinc-finger-DNA complexes have been compared to the NMR structure of the TGEKP linker connecting fingers 1 and 2 in zf1-3 in the absence of DNA. This comparison reveals that additional stabilization likely arises in the DNA complexes from hydrogen bonding between the backbone amide of E3 and the side-chain O(gamma) of T1 in the linker. We suggest that these DNA-induced C-capping interactions provide a means whereby the multiple-finger complex, which must necessarily be domain-flexible in the unbound state as it searches for the correct DNA sequence, can be "snap-locked" in place once the correct DNA sequence is encountered. These observations provide a rationale for the high conservation of the TGEKP linker sequences in Cys(2)-His(2) zinc finger proteins.

Structure-based design of an RNA-binding zinc finger

A structure-based approach was used to design RNA-binding zinc fingers that recognize the HIV-1 Rev response element (RRE). An arginine-rich alpha-helix from HIV-1 Rev was engineered into the zinc finger framework, and the designed fingers were shown to bind specifically to the RRE with high affinity and in a zinc-dependent manner, and display cobalt absorption and CD spectra characteristic of properly folded fingers. The results indicate that a monomeric zinc finger can recognize a specific nucleic acid site and that the alpha-helix of a finger can be used to recognize the major groove of RNA as well as DNA. The RRE-binding zinc fingers demonstrate how structure-based approaches may be used in the design of potential RNA-binding therapeutics and provide a framework for selecting RNA-binding fingers with desired specifications.

Solution structure of the transactivation domain of ATF-2 comprising a zinc finger-like subdomain and a flexible subdomain

Activating transcription factor-2 (ATF-2) is a transcription factor that binds to cAMP response element (CRE). ATF-2 contains two functional domains, an N-terminal transactivation domain and a C-terminal DNA-binding domain. The DNA-binding domain contains the basic leucine zipper (bZip) motif. Here, the three-dimensional structure of the transactivation domain of ATF-2 has been determined by NMR. The transactivation domain consists of two subdomains: the structure of an N-terminal half (N-subdomain) is well determined, while a C-terminal half (C-subdomain) takes a highly flexible and disordered structure. The architecture of the N-subdomain is very similar to that of the well-known zinc finger motif found in DNA-binding domains, consisting of an antiparallel beta-sheet and an alpha-helix. The zinc atom is tetrahedrally coordinated to two cysteine residues and two histidine residues. Amino acids that form the hydrophobic core in all of the DNA-binding zinc fingers are well conserved in the N-subdomain of the transactivation domain, whereas some amino acids that are responsible for binding to the phosphate backbone of DNA in the DNA-binding zinc fingers are substituted with other amino acids. The flexible C-subdomain, which contains two threonine residues that the stress-activated protein kinases phosphorylate, is likely to undergo a conformational change by specific binding to a target protein.

Zinc fingers in Caenorhabditis elegans: finding families and probing pathways

More than 3 percent of the protein sequences inferred from the Caenorhabditis elegans genome contain sequence motifs characteristic of zinc-binding structural domains, and of these more than half are believed to be sequence-specific DNA-binding proteins. The distribution of these zinc-binding domains among the genomes of various organisms offers insights into the role of zinc-binding proteins in evolution. In addition, the complete genome sequence of C. elegans provides an opportunity to analyze, and perhaps predict, pathways of transcriptional regulation.

Key residues characteristic of GATA N-fingers are recognized by FOG

Protein-protein interactions play significant roles in the control of gene expression. These interactions often occur between small, discrete domains within different transcription factors. In particular, zinc fingers, usually regarded as DNA-binding domains, are now also known to be involved in mediating contacts between proteins. We have investigated the interaction between the erythroid transcription factor GATA-1 and its partner, the 9 zinc finger protein, FOG (Friend Of GATA). We demonstrate that this interaction represents a genuine finger-finger contact, which is dependent on zinc-coordinating residues within each protein. We map the contact domains to the core of the N-terminal zinc finger of GATA-1 and the 6th zinc finger of FOG. Using a scanning substitution strategy we identify key residues within the GATA-1 N-finger which are required for FOG binding. These residues are conserved in the N-fingers of all GATA proteins known to bind FOG, but are not found in the respective C-fingers. This observation may, therefore, account for the particular specificity of FOG for N-fingers. Interestingly, the key N-finger residues are seen to form a contiguous surface, when mapped onto the structure of the N-finger of GATA-1.

Alterations in the GAL4 DNA-binding domain can affect transcriptional activation independent of DNA binding

The GAL4 protein belongs to a large class of fungal transcriptional activator proteins encoding within their DNA-binding domains (DBD) six cysteines that coordinate two atoms of zinc (the Zn2Cys6 domain). In an effort to characterize the interactions between the Zn2Cys6 class transcriptional activator proteins and their DNA-binding sites, we have replaced in the full-length GAL4 protein small regions of the Zn2Cys6 domain with the analogous regions of another Zn2Cys6 protein called PPR1 an activator of pyrimidine biosynthetic genes. Alterations between the first and third cysteines abolished binding to GAL4 (upstream activation sequence of GAL (UASG)) or PPR1 (upstream acitvation sequence of UAS) DNA-binding sites and severely reduced transcriptional activation in yeast. In contrast, alterations between the third and fourth cysteines had only minor effects on binding to UASG but led to substantial decreases in activation in both yeast and a mammalian cell line. In the crystal structure of the GAL4 DBD-UASG complex (Marmorstein, R., Carey, M., Ptashne, M., and Harrison, S. C. (1992) Nature 356, 408-414), this region is facing away from the DNA, making it likely that there exists within the GAL4 DBD an accessible domain important in activation.

Role of metal-ligand coordination in the folding pathway of zinc finger peptides

In the zinc fingers of TFIIIA family, two cysteines near the N-terminus and two histidines near the C-terminus are conserved for each finger unit. A cooperative binding of these residues to a Zn(II) ion is essential for the formation of the finger structure consisting of an anti-parallel beta-sheet and an alpha-helix. In order to reveal the folding pathway of the zinc finger, we have investigated, by Raman spectroscopy, the relationship between Zn(II)-ligand binding and conformational change of a 27-mer peptide representing the third finger of mouse transcription factor Zif268. In the absence of Zn(II), the peptide assumes a beta-sheet-rich structure. Upon addition of Zn(II), cysteines preferentially bind to Zn(II) prior to the metal coordination of histidines. Both the Zn(II)-cysteine and Zn(II)-histidine binding induce a partial secondary structure transition from beta-sheet to alpha-helix. Exchange of the ligand amino acid residues, i.e., cysteines to histidines and vice versa, produces a striking effect on the folding of the peptide. The beta-sheet-->alpha-helix transition is induced only by the Zn(II)-cysteine binding and the ligand exchanged peptide is not capable of folding into the finger structure. The present results demonstrate the importance of the ligand arrangement in the folding of zinc finger.

Molecular cloning and characterization of FHL2, a novel LIM domain protein preferentially expressed in human heart

A full-length cDNA clone encoding a novel LIM-only protein was isolated and sequenced from a human fetal heart cDNA library. This full-length clone consists of 1416 base pairs and has a predicted open reading frame (ORF) encoding 279 amino acids. The ORF of this polypeptide codes for the human heart-specific four and a half LIM-only protein 2 (FHL2). It possesses an extra zinc finger that is a half LIM domain and four repeats of LIM domain. When the human FHL2 cDNA probe was used to hybridize with poly-A RNA of various human tissues, a very strong signal could be seen in heart tissues, and only moderately low signals could be detected in placenta, skeletal muscle and ovary. Virtually no signal could be detected in brain, lung, liver, kidney, pancreas, spleen, thymus, prostate, testis, small intestine, colon or peripheral blood leukocyte. FHL2 was mapped to chromosome 2q12-q13 by fluorescent in-situ hybridization (FISH).

Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity and sequence specificity

The high resolution solution structure of a protein containing the three amino-terminal zinc fingers of Xenopus laevis transcription factor IIIA (TFIIIA) bound to its cognate DNA duplex was determined by nuclear magnetic resonance spectroscopy. The protein, which is designated zf1-3, binds with all three fingers in the DNA major groove, with a number of amino acids making base-specific contacts. The DNA structure is close to B-form. Although the mode of interaction of zf1-3 with DNA is similar to that of zif268 and other structurally characterized zinc finger complexes, the TFIIIA complex exhibits several novel features. Each zinc finger contacts four to five base-pairs and the repertoire of known base contact residues is extended to include a tryptophan at position +2 of the helix (finger 1) and arginine at position +10 (finger 3). Sequence-specific base contacts are made over virtually the entire length of the finger 3 helix. Lysine and histidine side-chains involved in base recognition are dynamically disordered in the solution structure; in the case of lysine, in particular, this could significantly decrease the entropic cost of DNA binding. The TGEKP(N) linker sequences, which are highly flexible in the unbound protein, adopt ordered conformations on DNA binding. The linkers appear to play an active structural role in stabilization of the protein-DNA complex. Substantial protein-protein contact surfaces are formed between adjacent fingers. As a consequence of these protein-protein interactions, the orientation of finger 1 in the major groove differs from that of the other fingers. Contributions to high affinity binding by zf1-3 come from both direct protein-DNA contacts and from indirect protein-protein interactions associated with structural organization of the linkers and formation of well-packed interfaces between adjacent zinc fingers in the DNA complex. The structures provide a molecular level explanation for the large body of footprinting and mutagenesis data available for the TFIIIA-DNA complex.

Synthesis and DNA-binding ability of Sp1 protein zinc finger domain and its peptidomimetics

The second zinc finger fragment of Sp1 (Sp1-ZF2), its mutant (Sp1-ZF2/HT. E(20) --> H, R(23) --> T), and two mimic analogues (ZF20 and ZF15) were synthesized by stepwise solid phase technique. The CD spectra and UV-visible spectrum with CoC1(2) indicated that the formation of zinc finger structure was affected not only by the hydrophobic amino acids but also by the change of the distance between Cys and His. Gel-retardat ion electrophoresis assays indicated that the Glu and Arg residues are very important for recognition. A single zinc finger like Sp1-ZF2 is able to bind DNA sequence specifically.

NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from the yeast transcription factor ADR1

Mutagenesis studies have revealed that the minimal DNA-binding domain of the yeast transcription factor ADR1 consists of two Cys2-His2 zinc fingers plus an additional 20 residues proximal and N-terminal to the fingers. We have assigned NMR 1H, 15N, and 13C chemical shifts for the entire minimal DNA-binding domain of ADR1 both free and bound to specific DNA. 1H chemical shift values suggest little structural difference between the zinc fingers in this construct and in single-finger constructs, and 13C alpha chemical shift index analysis indicates little change in finger structure upon DNA binding. 1H chemical shift perturbations upon DNA binding are observed, however, and these are mapped to define the protein-DNA interface. The two zinc fingers appear to bind DNA with different orientations, as the entire helix of finger 1 is perturbed, while only the extreme N-terminus of the finger 2 helix is affected. Furthermore, residues N-terminal to the first finger undergo large chemical shift changes upon DNA binding suggesting a role at the protein-DNA interface. A striking correspondence is observed between the protein-DNA interface mapped by chemical shift changes and that previously mapped by mutagenesis.

Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA

The three N-terminal zinc fingers of transcription factor IIIA bind in the DNA major groove. Substantial packing interfaces are formed between adjacent fingers, the linkers lose their intrinsic flexibility upon DNA binding, and several lysine side chains implicated in DNA recognition are dynamically disordered.

Structures of zinc finger domains from transcription factor Sp1. Insights into sequence-specific protein-DNA recognition

The carboxyl terminus of transcription factor Sp1 contains three contiguous Cys2-His2 zinc finger domains with the consensus sequence Cys-X2-4-Cys-X12-His-X3-His. We have used standard homonuclear two-dimensional NMR techniques to solve the solution structures of synthetic peptides corresponding to the last two zinc finger domains (Sp1f2 and Sp1f3, respectively) of Sp1. Our studies indicate a classical Cys2-His2 type fold for both the domains differing from each other primarily in the conformation of Cys-X2-Cys (beta-type I turn) and Cys-X4-Cys (beta-type II turn) elements. There are, however, no significant differences in the metal binding properties between the Cys-X4-Cys (Sp1f2) and Cys-X2-Cys (Sp1f3) subclasses of zinc fingers. The free solution structures of Sp1f2 and Sp1f3 are very similar to those of the analogous fingers of Zif268 bound to DNA. There is NMR spectral evidence suggesting that the Arg-Asp buttressing interaction observed in the Zif-268.DNA complex is also preserved in unbound Sp1f2 and Sp1f3. Modeling Sp1-DNA complex by overlaying the Sp1f2 and Sp1f3 structures on Zif268 fingers 1 and 2, respectively, predicts the role of key amino acid residues, the interference/protection data, and supports the model of Sp1-DNA interaction proposed earlier.

A CCHC metal-binding domain in Nanos is essential for translational regulation

The Drosophila Nanos protein is a localized repressor of hunchback mRNA translation in the early embryo, and is required for the establishment of the anterior-posterior body axis. Analysis of nanos mutants reveals that a small, evolutionarily conserved, C-terminal region is essential for Nanos function in vivo, while no other single portion of the Nanos protein is absolutely required. Within the C-terminal region are two unusual Cys-Cys-His-Cys (CCHC) motifs that are potential zinc-binding sites. Using absorption spectroscopy and NMR we demonstrate that the CCHC motifs each bind one equivalent of zinc with high affinity. nanos mutations disrupting metal binding at either of these two sites in vitro abolish Nanos translational repression activity in vivo. We show that full-length and C-terminal Nanos proteins bind to RNA in vitro with high affinity, but with little sequence specificity. Mutations affecting the hunchback mRNA target sites for Nanos-dependent translational repression were found to disrupt translational repression in vivo, but had little effect on Nanos RNA binding in vitro. Thus, the Nanos zinc domain does not specifically recognize target hunchback RNA sequences, but might interact with RNA in the context of a larger ribonucleoprotein complex.

Lessons from zinc-binding peptides

Zinc-finger domains are small metal-binding modules that are found in a wide range of gene regulatory proteins. Peptides corresponding to these domains have provided valuable model systems for examining a number of biophysical parameters entirely unrelated to their nucleic acid binding properties. These include the chemical basis for metal-ion affinity and selectivity, thermodynamic properties related to hydrophobic packing and beta-sheet propensities, and constraints on the generation of ligand-binding and potential catalytic sites. These studies have laid the foundation for applications such as the generation of optically detected zinc probes and the design of metal-binding peptides and proteins with desired spectroscopic and chemical properties.