Determination of the pK(a) of the four Zn2+-coordinating residues of the distal finger motif of the HIV-1 nucleocapsid protein: consequences on the binding of Zn2+

Relations between Structure and Zn(II) Binding Affinity Shed Light on the Mechanisms of Rad50 Hook Domain Functioning and Its Phosphorylation

The metal binding at protein–protein interfaces is still uncharted territory in intermolecular interactions. To date, only a few protein complexes binding Zn(II) in an intermolecular manner have been deeply investigated. The most notable example of such interfaces is located in the highly conserved Rad50 protein, part of the Mre11-Rad50-Nbs1 (MRN) complex, where Zn(II) is required for homodimerization (Zn(Rad50)2). The high stability of Zn(Rad50)2 is conserved not only for the protein derived from the thermophilic archaeon Pyrococcus furiosus (logK12 = 20.95 for 130-amino-acid-long fragment), which was the first one studied, but also for the human paralog studied here (logK12 = 19.52 for a 183-amino-acid-long fragment). As we reported previously, the extremely high stability results from the metal-coupled folding process where particular Rad50 protein fragments play a critical role. The sequence–structure–stability analysis based on human Rad50 presented here separates the individual structural components that increase the stability of the complex, pointing to amino acid residues far away from the Zn(II) binding site as being largely responsible for the complex stabilization. The influence of the individual components is very well reflected by the previously published crystal structure of the human Rad50 zinc hook (PDB: 5GOX). In addition, we hereby report the effect of phosphorylation of the zinc hook domain, which exerts a destabilizing effect on the domain. This study identifies factors governing the stability of metal-mediated protein–protein interactions and illuminates their molecular basis.

Metal binding properties of zinc fingers with a naturally altered metal binding site

Zinc fingers (ZFs) are among the most abundant motifs found in proteins, and are commonly known for their structural role. Classical ZFs (CCHH) are part of the transcription factors that participate in DNA binding. Although biochemical studies of classical ZFs have a long history, there is limited knowledge about the sequential and structural diversity of ZFs. We have found that classical ZFs, with metal binding sites consisting of amino acids other than conserved Cys or His residues, are frequently encoded in the human genome, and we refer to these peptides as ZFs with a naturally altered metal binding site. The biological role of the altered ZFs remains undiscovered. In this study, we characterized nine natural XCHH, CXHH, CCXH and CCHX ZFs in terms of their Zn(ii) and Co(ii) binding properties, such as complex stoichiometry, spectroscopic properties and metal-to-peptide affinity. We revealed that XCHH and CXHH ZFs form ML complexes that are 4-5 orders of magnitude weaker in comparison to CCHH ZFs. Nevertheless, spectroscopic studies demonstrate that, depending on the altered position, they may adopt an open coordination geometry with one or two water molecules bound to a central metal ion, which has not been demonstrated in natural ZFs before. Stability data show that both CCXH and CCHX peptides have high Zn(ii) affinity (with a K_d of 10^-9 to 10^-11 M), suggesting their potential biological function. This study is a comprehensive overview of the relationship between the sequence, structure, and stability of ZFs.

Temperature effect on the structure and conformational fluctuations in two zinc knuckles from the mouse mammary tumor virus

Zinc fingers are small protein domains in which zinc plays a structural role, contributing to the stability of the zinc-peptide complex. Zinc fingers are structurally diverse and are present in proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and translation, metabolism and signaling, cell proliferation, and apoptosis. Zinc fingers typically function as interaction modules and bind to a wide variety of compounds, such as nucleic acids, proteins, and small molecules. In this study, we investigated the structural properties, in solution, of the proximal and distal zinc knuckles of the nucleocapsid (NC) protein from the mouse mammary tumor virus (MMTV) (MMTV NC). For this purpose, we performed a series of molecular dynamics simulations in aqueous solution at 300 K, 333 K, and 348 K. The temperature effect was evaluated in terms of root mean square deviation of the backbone atoms and root mean square fluctuation of the coordinating residue atoms. The stability of the zinc coordination sphere was analyzed based upon the time profile of the interatomic distances between the zinc ions and the chelator atoms. The results indicate that the hydrophobic character of the proximal zinc finger is dominant at 333 K. The low mobility of the coordinating residues suggests that the strong electrostatic effect exerted by the zinc ion on its coordinating residues is not influenced by the increase in temperature. The evolution of the structural parameters of the coordination sphere of the distal zinc finger at 300 K gives us a reasonable picture of the unfolding pathway, as proposed by Bombarda and coworkers (Bombarda et al., 2005), which can predict the binding order of the four conserved ligand-binding residues. Our results support the conclusion that the structural features can vary significantly between the two zinc knuckles of MMTV NC.

Molar absorption coefficients and stability constants of Zincon metal complexes for determination of metal ions and bioinorganic applications

Zincon (ZI) is one of the most common chromophoric chelating probes for the determination of Zn²⁺ and Cu²⁺ ions. It is also known to bind other metal ions. However, literature data on its binding properties and molar absorption coefficients are rather poor, varying among publications or determined only in certain conditions. There are no systematic studies on Zn²⁺ and Cu²⁺ affinities towards ZI performed under various conditions. However, this widely commercially available and inexpensive agent is frequently the first choice probe for the measurement of metal binding and release as well as determination of affinity constants of other ligands/macromolecules of interest. Here, we establish the spectral properties and the stability of ZI and its complexes with Zn²⁺, Cu²⁺, Cd²⁺, Hg²⁺, Co²⁺, Ni²⁺ and Pb²⁺ at multiple pH values from 6 to 9.9. The obtained results show that in water solution the MZI complex is predominant, but in the case of Co²⁺ and Ni²⁺, M(ZI)₂ complexes are also formed. The molar absorption coefficient at 618 nm for ZnZI and 599nm for CuZI complexes at pH7.4 in buffered (I=0.1M) water solutions are 24,200 and 26,100M^-1cm^-1, respectively. Dissociation constants of those complexes are 2.09×10^-6 and 4.68×10^-17M. We also characterized the metal-assisted Zincon decomposition. Our results provide new and reassessed optical and stability data that are applicable to a wide range of chemical and bioinorganic applications including metal ion detection, and quantification and affinity studies of ligands of interest.

SYNOPSIS

Accurate values of molar absorption coefficients of Zincon complex with Zn²⁺, Cd²⁺, Hg²⁺, Co²⁺, Ni²⁺, Cu²⁺, and Pb²⁺ for rapid metal ion quantification are provided. Zincon stability constants with Zn²⁺ and Cu²⁺ in a wide pH range were determined.

Metal-coupled folding as the driving force for the extreme stability of Rad50 zinc hook dimer assembly

The binding of metal ions at the interface of protein complexes presents a unique and poorly understood mechanism of molecular assembly. A remarkable example is the Rad50 zinc hook domain, which is highly conserved and facilitates the Zn²⁺-mediated homodimerization of Rad50 proteins. Here, we present a detailed analysis of the structural and thermodynamic effects governing the formation and stability (logK₁₂ = 20.74) of this evolutionarily conserved protein assembly. We have dissected the determinants of the stability contributed by the small β-hairpin of the domain surrounding the zinc binding motif and the coiled-coiled regions using peptides of various lengths from 4 to 45 amino acid residues, alanine substitutions and peptide bond-to-ester perturbations. In the studied series of peptides, an >650 000-fold increase of the formation constant of the dimeric complex arises from favorable enthalpy because of the increased acidity of the cysteine thiols in metal-free form and the structural properties of the dimer. The dependence of the enthalpy on the domain fragment length is partially compensated by the entropic penalty of domain folding, indicating enthalpy-entropy compensation. This study facilitates understanding of the metal-mediated protein-protein interactions in which the metal ion is critical for the tight association of protein subunits.

Nucleocapsid Protein: A Desirable Target for Future Therapies Against HIV-1

The currently available anti-HIV-1 therapeutics is highly beneficial to infected patients. However, clinical failures occur as a result of the ability of HIV-1 to rapidly mutate. One approach to overcome drug resistance is to target HIV-1 proteins that are highly conserved among phylogenetically distant viral strains and currently not targeted by available therapies. In this respect, the nucleocapsid (NC) protein, a zinc finger protein, is particularly attractive, as it is highly conserved and plays a central role in virus replication, mainly by interacting with nucleic acids. The compelling rationale for considering NC as a viable drug target is illustrated by the fact that point mutants of this protein lead to noninfectious viruses and by the inability to select viruses resistant to a first generation of anti-NC drugs. In our review, we discuss the most relevant properties and functions of NC, as well as recent developments of small molecules targeting NC. Zinc ejectors show strong antiviral activity, but are endowed with a low therapeutic index due to their lack of specificity, which has resulted in toxicity. Currently, they are mainly being investigated for use as topical microbicides. Greater specificity may be achieved by using non-covalent NC inhibitors (NCIs) targeting the hydrophobic platform at the top of the zinc fingers or key nucleic acid partners of NC. Within the last few years, innovative methodologies have been developed to identify NCIs. Though the antiviral activity of the identified NCIs needs still to be improved, these compounds strongly support the druggability of NC and pave the way for future structure-based design and optimization of efficient NCIs.

Advances in targeting nucleocapsid-nucleic acid interactions in HIV-1 therapy

The continuing challenge of HIV-1 treatment resistance in patients creates a need for the development of new antiretroviral inhibitors. The HIV nucleocapsid (NC) protein is a potential therapeutic target. NC is necessary for viral RNA packaging and in the early stages of viral infection. The high level of NC amino acid conservation among all HIV-1 clades suggests a low tolerance for mutations. Thus, NC mutations that could arise during inhibitor treatment to provide resistance may render the virus less fit. Disruption of NC function provides a unique opportunity to strongly dampen replication at multiple points during the viral life cycle with a single inhibitor. Although NC exhibits desirable features for a potential antiviral target, the structural flexibility, size, and the presence of two zinc fingers makes small molecule targeting of NC a challenging task. In this review, we discuss the recent advances in strategies to develop inhibitors of NC function and present a perspective on potential novel approaches that may help to overcome some of the current challenges in the field.

On the design of zinc-finger models with cyclic peptides bearing a linear tail

Cyclic peptides with a linear tail (CPLT) have been successfully used to model two zinc fingers (ZFs) adopting the treble-clef- and loosened zinc-ribbon folds. In this article, we examine the factors that may influence the design of such ZF models: mutations in the sequence, size of the cycle, and size of the tail. For this purpose, several peptides derived from the CPLT-based models of the treble-clef- and loosened zinc-ribbon ZF were synthesized and studied. CPLT-based models appear to be robust toward mutations, accommodate various cycle sizes, and are sensible to the size of the linking region of the tail located between the cycle and the coordinating amino acids. Based on these criteria, we describe the design of a new CPLT-based model for the zinc-ribbon ZFs, LZR , and compare it to a linear analogue, LZR(lin) . The model complex Zn⋅LZR is able to fold correctly around the metal ion contrary to Zn⋅LZR(lin) , suggesting that CPLT-based models are more likely to yield structurally meaningful models of ZF sites than linear peptide models. Finally, we draw some rules that could allow the design of new CPLT-based metallopeptides with a controlled fold.

Reactive cysteine in the structural Zn(2+) site of the C1B domain from PKCα

Structural cysteine-rich Zn(2+) sites that stabilize protein folds are considered to be unreactive. In this article, we identified a reactive cysteine residue, Cys151, in a treble-clef zinc finger with a Cys(3)His coordination sphere. The protein in question is the C1B domain of Protein Kinase Cα (PKCα). Mass-tagging cysteine assays of several C1B variants were employed to ascertain the site specificity of the covalent modification. The reactivity of Cys151 in C1B also manifests itself in the structural dynamics of the Zn(2+) coordination sphere where the Sγ of Cys151 alternates between the Zn(2+)-bound thiolate and free thiol states. We used NMR-detected pH titrations, ZZ-exchange spectroscopy, and residual dipolar coupling (RDC)-driven structure refinement to characterize the two exchanging conformations of C1B that differ in zinc coordination. Our data suggest that Cys151 serves as an entry point for the reactive oxygen species that activate PKCα in a process involving Zn(2+) release.

Thermodynamics of Zn2+ binding to Cys2His2 and Cys2HisCys zinc fingers and a Cys4 transcription factor site

The thermodynamics of Zn(2+) binding to three peptides corresponding to naturally occurring Zn-binding sequences in transcription factors have been quantified with isothermal titration calorimetry (ITC). These peptides, the third zinc finger of Sp1 (Sp1-3), the second zinc finger of myelin transcription factor 1 (MyT1-2), and the second Zn-binding sequence of the DNA-binding domain of glucocorticoid receptor (GR-2), bind Zn(2+) with Cys(2)His(2), Cys(2)HisCys, and Cys(4) coordination, respectively. Circular dichroism confirms that Sp1-3 and MyT1-2 have considerable and negligible Zn-stabilized secondary structure, respectively, and indicate only a small amount for GR-2. The pK(a)'s of the Sp1-3 cysteines and histidines were determined by NMR and used to estimate the number of protons displaced by Zn(2+) at pH 7.4. ITC was also used to determine this number, and the two methods agree. Subtraction of buffer contributions to the calorimetric data reveals that all three peptides have a similar affinity for Zn(2+), which has equal enthalpy and entropy components for Sp1-3 but is more enthalpically disfavored and entropically favored with increasing Cys ligands. The resulting enthalpy-entropy compensation originates from the Zn-Cys coordination, as subtraction of the cysteine deprotonation enthalpy results in a similar Zn(2+)-binding enthalpy for all three peptides, and the binding entropy tracks with the number of displaced protons. Metal and protein components of the binding enthalpy and entropy have been estimated. While dominated by Zn(2+) coordination to the cysteines and histidines, other residues in the sequence affect the protein contributions that modulate the stability of these motifs.

Femtomolar Zn2+ affinity of LIM domain of PDLIM1 protein uncovers crucial contribution of protein-protein interactions to protein stability

An individual LIM domain has approximately 55 amino acids with 8 highly conserved residues responsible for binding of two Zn(2+) into two distinct zinc finger motifs. We examined LIM domain stability of PDLIM1 protein (known also as Elfin protein), its C-terminally extended constructs as well as separate zinc fingers, and several full domain mutants in terms of Zn(2+) affinity and domain stability. Thermal denaturation, mass spectrometry, limited proteolysis, protein oxidation and circular dichroism techniques were used to determine a set of thermodynamic stability parameters. The results demonstrate unambiguously very high (femtomolar) affinity of both Zn(2+) to the conserved LIM domain (K(d)(av)=2.5×10(-14) M) and its additional elevation in the C-terminally extended domain construct (K(d)(av)=3.1×10(-15) M). We demonstrate in the example of PDLIM1 using a set of LIM protein constructs and its zinc finger peptides that stability of the entire zinc-containing domain is not only defined by the Zn(2+) coordination environment but significantly depends on the set of protein-protein interactions with the C-terminus of the protein. We discuss structural similarities of LIM domains and suggest the prolongation of the conserved LIM sequence to its C-terminal helix that has a significant impact on domain stability. We also discuss the functionality of LIM domains in terms of different physiological zinc and redox buffering capacity.

Use of virtual screening for discovering antiretroviral compounds interacting with the HIV-1 nucleocapsid protein

The HIV-1 nucleocapsid protein (NC) is considered as an emerging drug target for the therapy of AIDS. Several studies have highlighted the crucial role of NC within the viral replication cycle. However, although NC inhibition has provided in vitro and in vivo antiretroviral activity, drug-candidates which interfere with NC functions are still missing in the therapeutic arsenal against HIV. Based on previous studies, where the dynamic behavior of NC and its ligand binding properties have been investigated by means of computational methods, here we used a virtual screening protocol for discovering novel antiretroviral compounds which interact with NC. The antiretroviral activity of virtual hits was tested in vitro, whereas biophysical studies elucidated the direct interaction of most active compounds with NC(11-55), a peptide corresponding to the zinc finger domain of NC. Two novel antiretroviral small molecules capable of interacting with NC are presented here.

Solution structure of RING finger-like domain of retinoblastoma-binding protein-6 (RBBP6) suggests it functions as a U-box

Retinoblastoma-binding protein-6 (RBBP6) plays a facilitating role, through its RING finger-like domain, in the ubiquitination of p53 by Hdm2 that is suggestive of E4-like activity. Although the presence of eight conserved cysteine residues makes it highly probable that the RING finger-like domain coordinates two zinc ions, analysis of the primary sequence suggests an alternative classification as a member of the U-box family, the members of which do not bind zinc ions. We show here that despite binding two zinc ions, the domain adopts a homodimeric structure highly similar to those of a number of U-boxes. Zinc ions could be replaced by cadmium ions without significantly disrupting the structure or the stability of the domain, although the rate of substitution was an order of magnitude slower than any previous measurement, suggesting that the structure is particularly stable, a conclusion supported by the high thermal stability of the domain. A hallmark of U-box-containing proteins is their association with chaperones, with which they cooperate in eliminating irretrievably unfolded proteins by tagging them for degradation by the proteasome. Using a yeast two-hybrid screen, we show that RBBP6 interacts with chaperones Hsp70 and Hsp40 through its N-terminal ubiquitin-like domain. Taken together with the structural similarities to U-box-containing proteins, our data suggest that RBBP6 plays a role in chaperone-mediated ubiquitination and possibly in protein quality control.

Interaction of arsenite with a zinc finger CCHC peptide: evidence for formation of an As-Zn-peptide mixed complex

The interaction of arsenite with a Cys(3)His (CCHC) zinc finger model (34-51) HIV-1 nucleocapsid protein p7 (NCp7) peptide in the absence and presence of Zn(II) was studied using fluorescence spectroscopy, CD (circular dichroism) and ESI-MS (Electrospray Ionization Mass Spectrometry). We found that arsenic forms different complexes with the free peptide and the zinc finger peptide. In the former case the peptide conformation differed greatly from that of the zinc finger, whereas in the second case a mixed As-Zn-peptide complex was formed with partial preservation of zinc finger conformation. An apparent stability constant was estimated for the mixed As-Zn-peptide complex (K=2083 M(-1) and 442 M(-1) at 25°C and pHs 6 and 7, respectively). Our study also shows that the interaction of arsenic with the CCHC motif is facilitated by glutathione (GSH), through formation of a GS-As-peptide conjugate.

Titration_DB: storage and analysis of NMR-monitored protein pH titration curves

NMR-monitored pH titration experiments are routinely used to measure site-specific protein pKa values. Accurate experimental pKa values are essential in dissecting enzyme catalysis, in studying the pH-dependence of protein stability and ligand binding, in benchmarking pKa prediction algorithms, and ultimately in understanding electrostatic effects in proteins. However, due to the complex ways in which pH-dependent electrostatic and structural changes manifest themselves in NMR spectra, reported apparent pKa values are often dependent on the way that NMR pH-titration curves are analyzed. It is therefore important to retain the raw NMR spectroscopic data to allow for documentation and possible re-interpretation. We have constructed a database of primary NMR pH-titration data, which is accessible via a web interface. Here, we report statistics of the database contents and analyze the data with a global perspective to provide guidelines on best practice for fitting NMR titration curves. Titration_DB is available at http://enzyme.ucd.ie/Titration_DB. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

The nucleocapsid protein of HIV-1 as a promising therapeutic target for antiviral drugs

The nucleocapsid protein (NCp7) is a major HIV-1 structural protein that plays key roles in viral replication, mainly through its conserved zinc fingers that direct specific interactions with the viral nucleic acids. Owing to its high degree of conservation and critical functions, NCp7 represents a target of choice for drugs that can potentially complement HAART, thus possibly impairing the circulation of drug-resistant HIV-1 strains. Zinc ejectors showing potent antiretroviral activity were developed, but early generations suffered from limited selectively and significant toxicity. Compounds with improved selectivity have been developed and are being explored as topical microbicide candidates. Several classes of molecules inhibiting the interaction of NCp7 with the viral nucleic acids have also been developed. Although small molecules would be more suited for drug development, most molecules selected by screening showed limited antiretroviral activity. Peptides and RNA aptamers appear to be more promising, but the mechanism of their antiretroviral activity remains elusive. Substantial and more concerted efforts are needed to further develop anti-HIV drugs targeting NCp7 and bring them to the clinic.

A fast and accurate method for predicting pKa of residues in proteins

Predicting the pH-activities of residues in proteins is an important problem in enzyme engineering and protein design. A novel predictor called 'Pred-pK(a)' was developed based on the physicochemical properties of amino acids and protein 3D structure. The Pred-pK(a) approach considers the influence of all other residues of the protein to predict the pK(a) value of an ionizable residue. An empirical equation was formulated, in which the pK(a) value was a distance-dependent function of physicochemical parameters of 20 amino acid types, describing their electrostatic and van der Waals interaction, as well as the effects of hydrogen bonds and solvation. Two sets of coefficients, {a(alpha)} and {b(l)}, were used in the predictor: {a(alpha)} is the weight factors of 20 amino acid types and {b(l)} is the weight factors of physicochemical properties of amino acids. An iterative double least square procedure was proposed to solve the two sets of weight factors alternately and iteratively in a training set. The two coefficient sets {a(alpha)} and {b(l)} thus obtained were used to predict the pK(a) values of residues in a protein. The average predictive error is +/-0.6 pH in less than a minute in common personal computer.

Inhibition of HIV-1 replication by a bis-thiadiazolbenzene-1,2-diamine that chelates zinc ions from retroviral nucleocapsid zinc fingers

The human immunodeficiency virus type 1 (HIV-1) nucleocapsid p7 (NCp7) protein holds two highly conserved "CCHC" zinc finger domains that are required for several phases of viral replication. Basic residues flank the zinc fingers, and both determinants are required for high-affinity binding to RNA. Several compounds were previously found to target NCp7 by reacting with the sulfhydryl group of cysteine residues from the zinc fingers. Here, we have identified an N,N'-bis(1,2,3-thiadiazol-5-yl)benzene-1,2-diamine (NV038) that efficiently blocks the replication of a wide spectrum of HIV-1, HIV-2, and simian immunodeficiency virus (SIV) strains. Time-of-addition experiments indicate that NV038 interferes with a step of the viral replication cycle following the viral entry but preceding or coinciding with the early reverse transcription reaction, pointing toward an interaction with the nucleocapsid protein p7. In fact, in vitro, NV038 efficiently depletes zinc from NCp7, which is paralleled by the inhibition of the NCp7-induced destabilization of cTAR (complementary DNA sequence of TAR). A chemical model suggests that the two carbonyl oxygens of the esters in this compound are involved in the chelation of the Zn(2+) ion. This compound thus acts via a different mechanism than the previously reported zinc ejectors, as its structural features do not allow an acyl transfer to Cys or a thiol-disulfide interchange. This new lead and the mechanistic study presented provide insight into the design of a future generation of anti-NCp7 compounds.

Conformational changes in redox pairs of protein structures

Disulfides are conventionally viewed as structurally stabilizing elements in proteins but emerging evidence suggests two disulfide subproteomes exist. One group mediates the well known role of structural stabilization. A second redox-active group are best known for their catalytic functions but are increasingly being recognized for their roles in regulation of protein function. Redox-active disulfides are, by their very nature, more susceptible to reduction than structural disulfides; and conversely, the Cys pairs that form them are more susceptible to oxidation. In this study, we searched for potentially redox-active Cys Pairs by scanning the Protein Data Bank for structures of proteins in alternate redox states. The PDB contains over 1134 unique redox pairs of proteins, many of which exhibit conformational differences between alternate redox states. Several classes of structural changes were observed, proteins that exhibit: disulfide oxidation following expulsion of metals such as zinc; major reorganisation of the polypeptide backbone in association with disulfide redox-activity; order/disorder transitions; and changes in quaternary structure. Based on evidence gathered supporting disulfide redox activity, we propose disulfides present in alternate redox states are likely to have physiologically relevant redox activity.

Cooperative metal binding and helical folding in model peptides of treble-clef zinc fingers

Two peptides, L(TC) and L(TC)(T) have been synthesised to model the treble-clef zinc fingers encountered in many Zn(Cys)(4)-site-containing proteins. Both are cyclic peptides with a linear tail grafted on a glutamate side chain of the cycle. They differ by the length of this tail, which lacks five amino acids in L(TC)(T) compared to L(TC). Both peptides bind Zn(2+) and Co(2+) in 1:1 metal/peptide ratio and the structure of these complexes have been characterised by NMR, UV/Vis and CD spectroscopy. Both peptides fold the same way around the metal ion and they fully reproduce the classical fold of treble-clef zinc fingers and display an extended hydrogen-bond network around the coordinating sulfur atoms. The structures of the ML(TC) complexes reveal that the linear tail forms a short two-turn alpha-helix, present in the metallated form only. The formation of this helix constitutes a rare example of metal-induced folding. The second turn of this helix is composed of the five amino acids that are absent in L(TC)(T). The study of the pH-dependence of the Zn(2+) binding constants shows that the metal ion is bound by four cysteinates above pH 5.2 and the binding constants are the highest reported so far. Interestingly, the binding constant of Zn x L(TC) is about tenfold higher than that of Zn x L(TC)(T). This difference clearly indicates that the helix, present in Zn x L(TC) only, stabilises the Zn(2+) complex by about 1.2 kcal mol(-1). The origin of this stabilisation is ascribed to an electrostatic interaction between the [ZnS(4)](2-) centre and the helix. This reveals a cooperative effect: zinc binding allows the folding of the tail into a helix which, in turn, strengthens the zinc complex.

Identification by high throughput screening of small compounds inhibiting the nucleic acid destabilization activity of the HIV-1 nucleocapsid protein

Due to its highly conserved zinc fingers and its nucleic acid chaperone properties which are critical for HIV-1 replication, the nucleocapsid protein (NC) constitutes a major target in AIDS therapy. Different families of molecules targeting NC zinc fingers and/or inhibiting the binding of NC with its target nucleic acids have been developed. However, their limited specificity and their cellular toxicity prompted us to develop a screening assay to target molecules able to inhibit NC chaperone properties, and more specifically the initial NC-promoted destabilization of the nucleic acid secondary structure. Since this destabilization is critically dependent on the properly folded fingers, the developed assay is thought to be highly specific. The assay was based on the use of cTAR DNA, a stem-loop sequence complementary to the transactivation response element, doubly labelled at its 5' and 3' ends by a rhodamine 6G fluorophore and a fluorescence quencher, respectively. Addition of NC(12-55), a peptide corresponding to the zinc finger domain of NC, to this doubly-labelled cTAR, led to a partial melting of the cTAR stem, which increases the distance between the two labels and thus, restores the rhodamine 6G fluorescence. Thus, positive hits were detected through the decrease of rhodamine 6G fluorescence. An "in-house" chemical library of 4800 molecules was screened and five compounds with IC(50) values in the micromolar range have been selected. The hits were shown by mass spectrometry and fluorescence anisotropy titration to prevent binding of NC(12-55) to cTAR through direct interaction with the NC folded fingers, but without promoting zinc ejection. These non-zinc ejecting NC binders are a new series of anti-NC molecules that could be used to rationally design molecules with potential anti-viral activities.

Characterization of the cofactor-induced folding mechanism of a zinc-binding peptide using computationally designed mutants

Metals are the most commonly encountered protein cofactors, and they play important structural and functional roles in biology. In many cases, metal binding provides a major driving force for a polypeptide chain to fold. While there are many studies on the structure, stability, and function of metal-binding proteins, there are few studies focusing on understanding the kinetic mechanism of metal-induced folding. Herein, the Zn(2+)-induced folding kinetics of a small zinc-binding protein are studied; the CH1(1) peptide is derived from the first cysteine/histidine-rich region (CH1 domain) of the protein interaction domains of the transcriptional coregulator CREB-binding protein. Computational design is used to introduce tryptophan and histidine mutations that are structurally consistent with CH1(1); these mutants are studied using stopped-flow tryptophan fluorescence experiments. The Zn(2+)-induced CH1(1) folding kinetics are consistent with two parallel pathways, where the initial binding of Zn(2+) occurs at two sites. However, the initially formed Zn(2+)-bound complexes can proceed either directly to the folded state where zinc adopts a tetrahedral coordination or to an off-pathway misligated intermediate. While elimination of those ligands responsible for misligation simplifies the folding kinetics, it also leads to a decrease in the zinc binding constant. Therefore, these results suggest why these nonnative zinc ligands in the CH1(1) motif are conserved in several distantly related organisms and why the requirement for function can lead to kinetic frustration in folding. In addition, the loop closure rate of the CH1(1) peptide is determined based on the proposed model and temperature-dependent kinetic measurements.

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.

The role of quantum mechanics in structure-based drug design

Herein we will focus on the use of quantum mechanics (QM) in drug design (DD) to solve disparate problems from scoring protein-ligand poses to building QM QSAR models. Through the variational principle of QM we know that we can obtain a more accurate representation of molecular systems than classical models, and while this is not a matter of debate, it still has not been shown that the expense of QM approaches is offset by improved accuracy in DD applications. Objectively validating the improved applicability and performance of QM over classical-based models in DD will be the focus of research in the coming years along with research on the conformational sampling problem as it relates to protein-ligand complexes.

Specificity of acyl transfer from 2-mercaptobenzamide thioesters to the HIV-1 nucleocapsid protein

The HIV-1 nucleocapsid protein (NCp7) is a small, highly conserved protein with two zinc-binding domains that are essential for the protein's function. Molecules that bind to and inactivate NCp7 are currently being evaluated as new antiviral drugs. In particular, derivatives based on a 2-mercaptobenzamide thioester template have been shown to specifically eject zinc from the C-terminal zinc-binding domain (ZD2) of NCp7 via acyl transfer from the thioester to a cysteine sulfur. In this study, mutational analysis of the NCp7 amino acid sequence has been used to investigate the specificity of the interaction between ZD2 and a 2-mercaptobenzamide thioester compound using UV-vis spectroscopy and mass spectrometry to monitor the rate of metal ejection from NCp7 mutant peptides and sites of acylation, respectively. We were able to extend the previously reported mechanism of action of these thioester compounds to include a secondary S to N intramolecular acyl transfer that occurs after the primary acyl transfer from the thioester to a cysteine side chain in the protein. Structural models of the thioester/ZD2 complex were then examined to identify the most likely binding orientation. We determined that position x+1 (where x is Cys36) needs to be an aromatic residue for reactivity and a hydrogen-bond donor in position x+9 is important for optimal reactivity. A basic residue (lysine or arginine) is required at position x+2 for the correct fold, while a lysine residue is needed for reactivity involving S to N acyl transfer. We report highly specific interactions between 2-mercaptobenzamide thioester compounds and NCp7 that offer a structural basis for refining and designing new antiretroviral therapeutics, directed toward a target that is resistant to viral mutation.

Determination of Residue-Specific Acid Dissociation Constants for Peptides By Band-Selective Homonuclear-Decoupled 1H NMR

Acid dissociation constants of side-chain acidic groups of amino acid residues in peptides can be determined by 1H NMR, provided resonances can be resolved for carbon-bonded reporter protons located near the acidic group. We report here that the increased resolution of the band-selective homonuclear-decoupled (BASHD) TOCSY experiment greatly extends the range of application of the NMR method for determination of residue-specific, side-chain acid dissociation constants of peptides that contain multiple residues of the same amino acid. Chemical shift-pH titration curves are obtained from cross-peaks for reporter protons in BASHD-TOCSY spectra measured as a function of pH. The method is based on using sequence-dependent differences in the chemical shifts of resonances for the backbone CalphaH protons and the increased resolution in BASHD-TOCSY spectra from collapse of CalphaH multiplets to singlets in the F1 dimension to resolve resonances for the side-chain reporter protons. Application of the method is demonstrated by determination of residue-specific pKA values for each of the side-chain ammonium groups of the six lysine residues in the hexadecapeptide Ac-SRGKAKVKAKVKDQTK-NH2. Chemical shift-pH titration curves were obtained for the lysine side-chain CepsilonH2 reporter protons from their resolved CalphaH-CepsilonH2 TOCSY cross-peaks in BASHD-TOCSY spectra. Relative acidities of the six ammonium groups were also determined from the residue specific chemical shift-pH titration data by a pH-independent method, and calculation of fractional concentrations of protonation microspecies using the residue-specific pKAs is also described.

Molecular mechanism of the Zn2+-induced folding of the distal CCHC finger motif of the HIV-1 nucleocapsid protein

HIV-1 nucleocapsid protein, NCp7, contains two highly conserved CCHC zinc fingers. Binding of Zn(2+) drives NCp7 from an unfolded to a highly folded structure that is critical for its functions. Using the intrinsic fluorescence of Trp(37), we investigated, by the stopped-flow technique, the folding of NCp7 distal finger through the pH dependence of its Zn(2+) association and dissociation kinetics. Zn(2+) binding was found to involve four different paths associated with the four deprotonated states of the finger. Each binding path involves the rapid formation of an intermediate complex that is subsequently rearranged and stabilized in a rate-limiting step. The equilibrium and kinetic rate constants of the full Zn(2+)-binding process have been determined. At neutral pH, the preferential pathway for the Zn(2+)-driven folding implies Zn(2+) binding to the deprotonated Cys(36) and His(44) residues, in the bidentate state of the finger. The resulting intermediate is then converted with a rate constant of 500 s(-1) into a more suitably folded form, probably through a rearrangement of the peptide backbone around Zn(2+) to optimize the binding geometry. This form then rapidly leads to the final native complex, through deprotonation of Cys(39) and Cys(49) residues and intramolecular substitution of coordinated water molecules. Zn(2+) dissociation is also characterized by a multistep process and occurs fastest via the deprotonated Zn(2+)-bound bidentate state with a rate constant of 3 s(-1). Due to their critical role in folding, the intermediates identified for the first time in this study may constitute potential targets for HIV therapy.

Role of Protons in the Thermodynamic Contribution of a Zn(II)-Cys4 Site toward Metalloprotein Stability

The current limited understanding of the free energy contributions of metal-protein interactions toward metalloprotein stability is largely due to an inability to separate the energetics of the metal-ligand and protein-protein interactions. In order to elucidate the thermodynamic contribution of a Zn(II)-(S.Cys)4 site toward metalloprotein stability relevant to classic structural Zn(II) sites, the reaction of {Zn(II)(H2O)6}2+ with a minimal, unstructured, tetracysteine 16-mer peptide, GGG, is described. Isothermal titration fluorimetry over the pH range of 4.5 to 9.0 is used to measure the free energy of Zn(II) binding to the model peptide GGG. The data show that, in the absence of proton competition, Zn(II) binds to the Cys4 coordination sphere with a Kd of 60 aM, indicating that the Zn(II)-(S.Cys)4 interaction can provide up to 22.1 kcal mol-1 in driving force for protein stabilization, folding, and/or assembly. Isothermal titration calorimetry shows that Zn(II)-GGG formation is entropy driven because of water release from both the metal and the peptide scaffold. At pH 7.0, where the Zn(II)-GGG Kd value is 8.0 pM, the reaction releases 3.8 protons, is endothermic with DeltaHrxn of +6.4 kcal mol-1, and entropy driven with DeltaSrxn of +72 cal K-1 mol-1. At pH 8.0, where the peptide is partially deprotonated prior to Zn(II) binding, the 1.0 fM Zn(II)-GGG Kd value reflects a Zn(II) complexation reaction involving the release of 2.5 protons, which is slightly exothermic, with DeltaHrxn of -2.0 kcal mol-1, and largely entropy driven, with DeltaSrxn of +61 cal K-1 mol-1. At pH 5.5, where proton competition weakens the Kd to 4.0 microM, only 3.2 protons are released upon Zn(II) binding, the reaction is endothermic, with DeltaHrxn of +7.7 kcal mol-1, and entropy driven, with DeltaSrxn of +51 cal K-1 mol-1. Likely an intrinsic property of Zn(II)-(S.Cys)4 sites, the entropy driven binding of Zn(II) reflects the proton dependent chemical speciation of the Zn(II)-(S.Cys)4 peptide complex and its effects on modulating the dehydration of both the peptide and metal. Furthermore, the Zn(II) binding thermodynamics of a variety of Zn(II) proteins at pH 7.0 reveals the presence of enthalpy-entropy compensation (EEC) phenomena in nature.

Femtomolar Zn(II) affinity in a peptide-based ligand designed to model thiolate-rich metalloprotein active sites

Metal-ligand interactions are critical components of metalloprotein assembly, folding, stability, electrochemistry, and catalytic function. Research over the past 3 decades on the interaction of metals with peptide and protein ligands has progressed from the characterization of amino acid-metal and polypeptide-metal complexes to the design of folded protein scaffolds containing multiple metal cofactors. De novo metalloprotein design has emerged as a valuable tool both for the modular synthesis of these complex metalloproteins and for revealing the fundamental tenets of metalloprotein structure-function relationships. Our research has focused on using the coordination chemistry of de novo designed metalloproteins to probe the interactions of metal cofactors with protein ligands relevant to biological phenomena. Herein, we present a detailed thermodynamic analysis of Fe(II), Co(II), Zn(II), and[4Fe-4S]2(+/+) binding to IGA, a 16 amino acid peptide ligand containing four cysteine residues, H2N-KLCEGG-CIGCGAC-GGW-CONH2. These studies were conducted to delineate the inherent metal-ion preferences of this unfolded tetrathiolate peptide ligand as well as to evaluate the role of the solution pH on metal-peptide complex speciation. The [4Fe-4S]2(+/+)-IGA complex is both an excellent peptide-based synthetic analogue for natural ferredoxins and is flexible enough to accommodate mononuclear metal-ion binding. Incorporation of a single ferrous ion provides the FeII-IGA complex, a spectroscopic model of a reduced rubredoxin active site that possesses limited stability in aqueous buffers. As expected based on the Irving-Williams series and hard-soft acid-base theory, the Co(II) and Zn(II) complexes of IGA are significantly more stable than the Fe(II) complex. Direct proton competition experiments, coupled with determinations of the conditional dissociation constants over a range of pH values, fully define the thermodynamic stabilities and speciation of each MII-IGA complex. The data demonstrate that FeII-IGA and CoII-IGA have formation constant values of 5.0 x 10(8) and 4.2 x 10(11) M-1, which are highly attenuated at physiological pH values. The data also evince that the formation constant for ZnII-IGA is 8.0 x 10(15) M-1, a value that exceeds the tightest natural protein Zn(II)-binding affinities. The formation constant demonstrates that the metal-ligand binding energy of a ZnII(S-Cys)4 site can stabilize a metalloprotein by -21.6 kcal/mol. Rigorous thermodynamic analyses such as those demonstrated here are critical to current research efforts in metalloprotein design, metal-induced protein folding, and metal-ion trafficking.

Co2+ Binding Cysteine and Selenocysteine: A DFT Study

In this paper we report structural and energetic data for cysteine and selenocysteine in the gas phase and the effect of Co(2+) complexation on their properties. Different conformers are analyzed at the DFT/B3LYP level of both bound and unbound species. Geometries, vibrational frequencies, and natural population analysis are reported and used to understand the activity of these species. In particular, we have focused our attention on the role of sulfur and selenium in the metal binding process and on the resulting deprotonation of the thiol and seleniol functions. From the present calculations we are able to explain, both from electronic structure and thermochemical point of views, a metal-induced thiol deprotonation as observed in gas-phase experiments. A similar process is expected in the case of selenocysteine. In fact, cobalt was found to have a preferential affinity with respect to thiolate and selenolate functions. This can be related to the observation that only S and Se are able-in thiolate and selenolate states-to make a partial charge transfer to the cobalt thus forming very stable complexes. Globally, very similar results are found when substituting S with Se, and a very small difference in cobalt binding affinity is found, thus justifying the use of this substitution in X-ray absorption experiments done on biomolecules containing cysteine metal binding pockets.

Toward a DFT-based molecular dynamics description of Co(ii) binding in sulfur-rich peptides

In this paper, we investigated the reliability of a Car-Parrinello molecular dynamics (CPMD) approach to characterize the binding of Co(II) metal cation to peptide molecules containing cysteine. To this end, we compared pseudo-potentials and DFT plane wave expansion, which are used as key ingredients in the CPMD method, with standard all-electron Gaussian basis set DFT calculations. The simulations presented here are the first attempts to characterize interactions and dynamics of Co(II) metal with the building blocks of phytochelatin peptide molecules. Benchmark calculations are performed on [Co(Cys-H)]+ and [Co(Glutathione-H)]+ complexes, since they are the main fragments of the Co(II)-Cys and Co(II)-glutathione systems found in gas phase electrospray ionisation mass spectrometry (ESI-MS) experiments done in our laboratory. We also present benchmark calculations on the [Co(H2O)6)]2+ cluster with direct comparisons to highly correlated ab initio calculations and experiments. In particular, we investigated the dissociation path of one water molecule from the first hydration shell of Co(II) with CPMD. Overall, our molecular dynamics simulations shed some light on the nature of the Co(II) interaction and reactivity in Co(II)-phytochelatin building block systems related to the biological and environmental activity of the metal, either in the gas or liquid phase.

Theoretical investigation of the behavior of titratable groups in proteins

This paper presents a theoretical analysis of the titration behavior of strongly interacting titratable residues in proteins. Strongly interacting titratable residues exist in many proteins such as for instance bacteriorhodopsin, cytochrome c oxidase, cytochrome bc(1), or the photosynthetic reaction center. Strong interaction between titratable groups can lead to irregular titration behavior. We analyze under which circumstances titration curves can become irregular. We demonstrate that conformational flexibility alone can not lead to irregular titration behavior. Strong interaction between titratable groups is a necessary, but not sufficient condition for irregular titration curves. In addition, the two interacting groups also need to titrate in the same pH-range. These two conditions together lead to irregular titration curves. The mutation of a single residue within a cluster of interacting titratable residues can influence the titration behavior of the other titratable residues in the cluster. We demonstrate this effect on a cluster of four interacting residues. This example underlines that mutational studies directed at identifying the role of a certain titratable residue in a cluster of interacting residues should always be accompanied by an analysis of the effect of the mutation on the titration behavior of the other residues.

Mechanism of Zinc Coordination by Point-Mutated Structures of the Distal CCHC Binding Motif of the HIV-1 NCp7 Protein†

The kinetics of Zn(2+) binding by two point-mutated forms of the HIV-1 NCp7 C-terminal zinc finger, each containing tridentate binding motif HCC [Ser49(35-50)NCp7] or CCC [Ala44(35-50)NCp7], has been studied by stopped-flow spectrofluorimetry. Both the formation and dissociation rate constants of the complexes between Zn(2+) and the two model peptides depend on pH. The results are interpreted on the basis of a multistep reaction model involving three Zn(2+) binding paths due to three deprotonated states of the coordinating motif, acting as monodentate, bidentate, and tridentate ligands. For Ser49(35-50)NCp7 around neutral pH, binding preferentially occurs via the deprotonated Cys36 in the bidentate state also involving His44. The binding rate constants for the monodentate and bidentate states are 1 x 10(6) and 3.9 x 10(7) M(-)(1) s(-)(1), respectively. For Ala44(35-50)NCp7, intermolecular Zn(2+) binding predominantly occurs via the deprotonated Cys36 in the monodentate state with a rate constant of 3.6 x 10(7) M(-)(1) s(-)(1). In both mutants, the final state of the Zn(2+) complex is reached by subsequent stepwise ligand deprotonation and intramolecular substitution of coordinated water molecules. The rate constants for the intermolecular binding paths of the bidentate and tridentate states of Ala44(35-50)NCp7 and of the tridentate state of Ser49(35-50)NCp7 are much smaller than expected according to electrostatic considerations. This is attributed to conformational constraints required to achieve proper metal coordination during folding. The dissociation of Zn(2+) from both peptides is again characterized by a multistep process and takes place fastest via the protonated Zn(2+)-bound bidentate and monodentate states, with rate constants of approximately 0.3 and approximately 10(3) s(-)(1), respectively, for Ser49(35-50)NCp7 and approximately 4 x 10(-)(3) and approximately 500 s(-)(1), respectively, for Ala44(35-50)NCp7.

Elimination of retroviral infectivity by N-ethylmaleimide with preservation of functional envelope glycoproteins

The zinc finger motifs in retroviral nucleocapsid (NC) proteins are essential for viral replication. Disruption of these Cys-X2-Cys-X4-His-X4-Cys zinc-binding structures eliminates infectivity. To determine if N-ethylmaleimide (NEM) can inactivate human immunodeficiency virus type 1 (HIV-1) or simian immunodeficiency virus (SIV) preparations by alkylating cysteines of NC zinc fingers, we treated infectious virus with NEM and evaluated inactivation of infectivity in cell-based assays. Inactivation was rapid and proportional to the NEM concentration. NEM treatment of HIV-1 or SIV resulted in extensive covalent modification of NC and other internal virion proteins. In contrast, viral envelope glycoproteins, in which the cysteines are disulfide bonded, remained intact and functional, as assayed by high-performance liquid chromatography, fusion-from-without analyses, and dendritic cell capture. Quantitative PCR assays for reverse transcription intermediates showed that NEM and 2,2'-dipyridyl disulfide (aldrithiol-2), a reagent which inactivates retroviruses through oxidation of cysteines in internal virion proteins such as NC, blocked HIV-1 reverse transcription prior to the formation of minus-strand strong-stop products. However, the reverse transcriptase from NEM-treated virions remained active in exogenous template assays, consistent with a role for NC in reverse transcription. Since disruption of NC zinc finger structures by NEM blocks early postentry steps in the retroviral infection cycle, virus preparations with modified NC proteins may be useful as vaccine immunogens and probes of the role of NC in viral replication.

Structure of the His44 → Ala Single Point Mutant of the Distal Finger Motif of HIV-1 Nucleocapsid Protein: A Combined NMR, Molecular Dynamics Simulation, and Fluorescence Study

The nucleocapsid protein (NCp7) of human immunodeficiency virus type 1 (HIV-1) contains two highly conserved CCHC zinc fingers that strongly bind Zn(2+) through coordination of one His and three Cys residues. It has been suggested that NCp7 function is conformation specific since substitution of any of the zinc coordinating residues in the zinc finger motifs leads to subsequent loss of viral infectivity. To further determine the structural requirements necessary for this specific conformation, we investigated by (1)H 2D NMR and molecular dynamics simulations the structure of the distal finger motif of NCp7 in which the zinc coordinating amino acid, His 44, was substituted by a noncoordinating Ala residue. While the fold of the N-terminal part of this mutated peptide was similar to that of the native peptide, an increased lability and significant conformational changes were observed in the vicinity of the His-to-Ala mutation. Moreover, molecular dynamics simulations suggested a mechanism by which the variant peptide can bind zinc ion even though one zinc-coordinating amino acid was lacking. Using the fluorescence of the naturally occurring Trp37 residue, the binding affinity of the variant peptide to the (TG)(3) model oligonucleotide was found to be decreased by about 2 orders of magnitude with respect with the native peptide. Modeling of the DNA:NCp7 complex using structures of the variant peptide suggests that the residues forming a hydrophobic cleft in the native protein are improperly oriented for efficient DNA binding by the variant peptide.

Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods

The characterization of electrostatic and chemical properties at the surface of biological macromolecules is of interest in elucidating the fundamental biological structure-function relationships as well as in problems of rational drug design. This paper presents a set of macromolecular quantum descriptors for the characterization of biological macromolecules in solution that can be obtained with modest computational cost from linear-scaling semi-empirical quantum/solvation methods. The descriptors discussed include: solvent-polarized electrostatic surface potential maps, equilibrated atomic charges, Fukui reactivity indices, approximate local hardness maps, and relative proton potentials. These properties are applied to study the conformational dependence of the electrostatic surface potential of the solvated phosphate-binding protein mutant (T141D), the regioselectivity of the zinc finger domains of HIV-1 nucleocapsid (NC) protein, and the order of pKa values of acidic residues in turkey ovomucoid third domain (OMTKY3) and of the zinc-binding residues in the carboxyl terminal zinc finger of NC. In all cases, insight beyond that obtainable from purely classical models is gained and can be used to rationalize the experimental observations. The macromolecular quantum descriptors presented here greatly extend the arsenal of tools for macromolecular characterization and offer promise in applications to modern structure-based drug design.

Spectropotentiometric analysis of metal binding to structural zinc-binding sites: accounting quantitatively for pH and metal ion buffering effects

Studies of the metal-binding affinity of protein sites are ubiquitous in bioinorganic chemistry and are valuable for the information that they can provide about metal speciation and exchange in biological systems. The potential for error in these studies is high, however, since many competing equilibria are present in solution and must be taken into consideration. Here, we report a new spectropotentiometric titration apparatus that allows pH and UV-vis absorption to be monitored simultaneously on small samples under inert atmosphere. In addition, we explain how data obtained from the complex equilibria can be combined with tabulated information about the protonation and metal-binding constants for common buffers to provide detailed, quantitative information about metal-protein interactions. Application of this approach to the investigation of metal binding to structural zinc-binding domains and common pitfalls encountered when performing these experiments are also discussed. We have used this approach to reevaluate the metal-binding constants of the N-terminal zinc-binding peptide from the HIV-1 nucleocapsid protein (10(-8)M</=K(d)(Co)</=10(-7)M; 10(-11)M</=K(d)(Zn)</=10(-10)M).

Insights into the regioselectivity and RNA-binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods

Human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein (NC) plays several important roles in the viral life-cycle and presents an attractive target for rational drug design. Here, the macromolecular reactivity of NC and its binding to RNA is characterized through determination of electrostatic and chemical descriptors derived from linear-scaling quantum calculations in solution. The computational results offer a rationale for the experimentally observed susceptibility of the Cys49 thiolate toward small-molecule electrophilic agents, and support the recently proposed stepwise protonation mechanism of the C-terminal Zn-coordination complex. The distinctive binding mode of NC to SL2 and SL3 stem-loops of the HIV-1 genomic RNA packaging signal is studied on the basis of protein side-chain contributions to the electrostatic binding energies. These results indicate the importance of several basic residues in the 3(10) helical region and the N-terminal zinc finger, and rationalize the presence of several evolutionarily conserved residues in NC. The combined reactivity and RNA-binding study provides new insights that may contribute toward the structure-based design of anti-HIV therapies.