Zinc Coordination Sphere Research Articles

Zinc Coordination Spheres in Protein Structures

Zinc metalloproteins are one of the most abundant and structurally diverse proteins in nature. In these proteins, the Zn(II) ion possesses a multifunctional role as it stabilizes the fold of small zinc fingers, catalyzes essential reactions in enzymes of all six classes, or assists in the formation of biological oligomers. Previously, a number of database surveys have been conducted on zinc proteins to gain broader insights into their rich coordination chemistry. However, many of these surveys suffer from severe flaws and misinterpretations or are otherwise limited. To provide a more comprehensive, up-to-date picture on zinc coordination environments in proteins, zinc containing protein structures deposited in the Protein Data Bank (PDB) were analyzed in detail. A statistical analysis in terms of zinc coordinating amino acids, metal-to-ligand bond lengths, coordination number, and structural classification was performed, revealing coordination spheres from classical tetrahedral cysteine/histidine binding sites to more complex binuclear sites with carboxylated lysine residues. According to the results, coordination spheres of hundreds of crystal structures in the PDB could be misinterpreted due to symmetry-related molecules or missing electron densities for ligands. The analysis also revealed increasing average metal-to-ligand bond length as a function of crystallographic resolution, which should be taken into account when interrogating metal ion binding sites. Moreover, one-third of the zinc ions present in crystal structures are artifacts, merely aiding crystal formation and packing with no biological significance. Our analysis provides solid evidence that a minimal stable zinc coordination sphere is made up by four ligands and adopts a tetrahedral coordination geometry.

Mononuclear and polynuclear 5-coordinate zinc(II) model complexes: a quantum chemical calibration study of their structure and energy

To further our understanding of the properties of zinc-seamed pyrogallol[4]arene nanocapsules, we have investigated the energetic and geometric properties of the model complexes Zn(C2O2H3)2Y, Y = NH3, C5H5N, CH3OH, (CH3)2NCHO, or (CH3)2SO, with a zinc coordination sphere representative of that in the capsules. The effect of the choice of density functional, basis set, and zinc pseudopotential on the equilibrium structures and Y ligand bond dissociation enthalpies has been assessed. Among the ways in which the suitability of these models has been confirmed was the construction of polynuclear zinc complexes having 2, 4, 6, or 8 metal ions combined with C2O2H3 −, C4O3H4 2−, and NH3 ligands, which indeed show that a closed ring is formed. The natural curvature of these complexes suggests that pentacoordination of Zn may be a key factor in seaming the pre-existing cone-shaped pyrogallol[4]arenes to form dimer capsules.

Structure of components of an intercellular channel complex in sporulating Bacillus subtilis

Following asymmetric cell division during spore formation in Bacillus subtilis, a forespore expressed membrane protein SpoIIQ, interacts across an intercellular space with a mother cell-expressed membrane protein, SpoIIIAH. Their interaction can serve as a molecular "ratchet" contributing to the migration of the mother cell membrane around that of the forespore in a phagocytosis-like process termed engulfment. Upon completion of engulfment, SpoIIQ and SpoIIIAH are integral components of a recently proposed intercellular channel allowing passage from the mother cell into the forespore of factors required for late gene expression in this compartment. Here we show that the extracellular domains of SpoIIQ and SpoIIIAH form a heterodimeric complex in solution. The crystal structure of this complex reveals that SpoIIQ has a LytM-like zinc-metalloprotease fold but with an incomplete zinc coordination sphere and no metal. SpoIIIAH has an α-helical subdomain and a protruding β-sheet subdomain, which mediates interactions with SpoIIQ. SpoIIIAH has sequence and structural homology to EscJ, a type III secretion system protein that forms a 24-fold symmetric ring. Superposition of the structures of SpoIIIAH and EscJ reveals that the SpoIIIAH protomer overlaps with two adjacent protomers of EscJ, allowing us to generate a dodecameric SpoIIIAH ring by using structural homology. Following this superposition, the SpoIIQ chains also form a closed dodecameric ring abutting the SpoIIIAH ring, producing an assembly surrounding a 60 Å channel. The dimensions and organization of the proposed complex suggest it is a plausible model for the extracellular component of a gap junction-like intercellular channel.

Minimal Functional Sites Allow a Classification of Zinc Sites in Proteins

Zinc is indispensable to all forms of life as it is an essential component of many different proteins involved in a wide range of biological processes. Not differently from other metals, zinc in proteins can play different roles that depend on the features of the metal-binding site. In this work, we describe zinc sites in proteins with known structure by means of three-dimensional templates that can be automatically extracted from PDB files and consist of the protein structure around the metal, including the zinc ligands and the residues in close spatial proximity to the ligands. This definition is devised to intrinsically capture the features of the local protein environment that can affect metal function, and corresponds to what we call a minimal functional site (MFS). We used MFSs to classify all zinc sites whose structures are available in the PDB and combined this classification with functional annotation as available in the literature. We classified 77% of zinc sites into ten clusters, each grouping zinc sites with structures that are highly similar, and an additional 16% into seven pseudo-clusters, each grouping zinc sites with structures that are only broadly similar. Sites where zinc plays a structural role are predominant in eight clusters and in two pseudo-clusters, while sites where zinc plays a catalytic role are predominant in two clusters and in five pseudo-clusters. We also analyzed the amino acid composition of the coordination sphere of zinc as a function of its role in the protein, highlighting trends and exceptions. In a period when the number of known zinc proteins is expected to grow further with the increasing awareness of the cellular mechanisms of zinc homeostasis, this classification represents a valuable basis for structure-function studies of zinc proteins, with broad applications in biochemistry, molecular pharmacology and de novo protein design.

Belt-Shaped π-Systems: Relating Geometry to Electronic Structure in a Six-Porphyrin Nanoring

Linear π-conjugated oligomers have been widely investigated, but the behavior of the corresponding cyclic oligomers is poorly understood, despite the recent synthesis of π-conjugated macrocycles such as [n]cycloparaphenylenes and cyclo[n]thiophenes. Here we present an efficient template-directed synthesis of a π-conjugated butadiyne-linked cyclic porphyrin hexamer directly from the monomer. Small-angle X-ray scattering data show that this nanoring is shape-persistent in solution, even without its template, whereas the linear porphyrin hexamer is relatively flexible. The crystal structure of the nanoring-template complex shows that most of the strain is localized in the acetylenes; the porphyrin units are slightly curved, but the zinc coordination sphere is undistorted. The electrochemistry, absorption, and fluorescence spectra indicate that the HOMO-LUMO gap of the nanoring is less than that of the linear hexamer and less than that of the corresponding polymer. The nanoring exhibits six one-electron reductions and six one-electron oxidations, most of which are well resolved. Ultrafast fluorescence anisotropy measurements show that absorption of light generates an excited state that is delocalized over the whole π-system within a time of less than 0.5 ps. The fluorescence spectrum is amazingly structured and red-shifted. A similar, but less dramatic, red-shift has been reported in the fluorescence spectra of cycloparaphenylenes and was attributed to a high exciton binding energy; however the exciton binding energy of the porphyrin nanoring is similar to those of linear oligomers. Quantum-chemical excited state calculations show that the fluorescence spectrum of the nanoring can be fully explained in terms of vibronic Herzberg-Teller (HT) intensity borrowing.

Zinc–Homocysteine binding in cobalamin‐dependent methionine synthase and its role in the substrate activation: DFT, ONIOM, and QM/MM molecular dynamics studies

Cobalamin-dependent methionine synthase (MetH) is an important metalloenzyme responsible for the biosynthesis of methionine. It catalyzes methyl transfer from N(5)-methyl-tetrahydrofolate to homocysteine (Hcy) by using a zinc ion to activate the Hcy substrate. Density functional theory (B3LYP) calculations on the active-site model in gas phase and in a polarized continuum model were performed to study the Zn coordination changes from the substrate-unbound state to the substrate-bound state. The protein effect on the Zn(2+) coordination exchange was further investigated by ONIOM (B3LYP:AMBER)-ME and EE calculations. The Zn(2+)-coordination exchange is found to be highly unfavorable in the gas phase with a high barrier and endothermicity. In the water solution, the reaction becomes exothermic and the reaction barrier is drastically decreased to about 10.0 kcal/mol. A considerable protein effect on the coordination exchange was also found; the reaction is even more exothermic and occurs without barrier. The enzyme was suggested to constrain the zinc coordination sphere in the reactant state (Hcy-unbound state) more than that in the product state (Hcy-bound state), which promotes ligation of the Hcy substrate. Molecular dynamics simulations using molecular mechanics (MM) and PM3/MM potentials suggest a correlation between the flexibility of the Zn(2+)-binding site and regulation of the enzyme function. Directed in silico mutations of selected residues in the active site were also performed. Our studies support a dissociative mechanism starting with the Zn-O(Asn234) bond breaking followed by the Zn-S((Hcy)) bond formation; the proposed associative mechanism for the Zn(2+)-coordination exchange is not supported.

Synthesis and structural characterization of a zinc(II) complex of the mycobactericidal drug isoniazid – Toxicity against Artemia salina

A new zinc(II) complex of the mycobactericidal drug isoniazid (complex 1) was synthesized and characterized by XRD, vibrational spectroscopy (IR, Raman) and thermogravimetric analysis. The complex is constituted by two isoniazid (INH) molecules, six hydration water molecules and two perchlorate counter-ions for each metal center (C 12H 26N 6Cl 2O 16Zn). Zinc(II) adopts a distorted octahedral geometry, where two INH molecules coordinate in a bidentate manner through the hydrazide group (N, O) and the other two isoniazid residues complete the coordination sphere of zinc(II) through their aromatic nitrogen atoms. This coordination pattern gives rise to a 2-D coordination polymer. Complex 1 belongs to the monoclinic system [ a = 8.1190(2) Å, b = 17.977(4) Å, c = 9.1051(2) Å and β = 100.87(3)°], space group P2 1. A biological assay with Artemia salina was also performed. Complex 1 is almost 8.5 times more active than the free ligand. Its toxicity against A. salina correlates well with the cytotoxic activity for some human solid tumors. Therefore, antitumoral properties could be expected from complex 1.

Synthesis and Coordination Chemistry of Two N2-Donor Chelating Di(indazolyl)methane Ligands: Structural Characterization and Comparison of Their Metal Chelation Aptitudes

The N(2)-donor bidentate ligands di(1H-indazol-1-yl)methane (L(1)) and di(2H-indazol-2-yl)methane (L(2)) (L in general) have been synthesized, and their coordination behavior toward Zn(II), Cd(II), and Hg(II) salts has been studied. Reaction of L(1) and L(2) with ZnX(2) (X = Cl, Br, or I) yields [ZnX(2)L] species (1-6), that, in the solid state, show a tetrahedral structure with dihapto ligand coordination via the pyrazolyl arms. The reaction of L(1) and L(2) with Zn(NO(3))(2)·6H(2)O is strongly dependent on the reaction conditions and on the ligand employed. Reaction of L(1) with equimolar quantities of Zn(NO(3))(2)·6H(2)O yields the neutral six-coordinate species [Zn(NO(3))(2)(L(1))], 7. On the other hand the use of L(1) excess gives the 2:1 adduct [Zn(NO(3))(2)(L(1))(2)], 8 where both nitrates act as a unidentate coordinating ligand. Analogous stoichiometry is found in the compound obtained from the reaction of L(2) with Zn(NO(3))(2)·6H(2)O which gives the ionic [Zn(NO(3))(L(2))(2)](NO(3)), 10. Complete displacement of both nitrates from the zinc coordination sphere is observed when the reaction between L(1) excess and the zinc salt was carried out in hydrothermal conditions. The metal ion type is also determining structure and stoichiometry: the reaction of L(2) with CdCl(2) gave the 2:1 adduct [CdCl(2)(L(2))(2)] 11 where both chlorides complete the coordination sphere of the six-coordinate cadmium center; on the other hand from the reaction of L(1) with CdBr(2) the polynuclear [CdBr(2)(L(1))](n) 12 is obtained, the Br(-) anion acting as bridging ligands in a six-coordinate cadmium coordination environment. The reaction of L(1) and L(2) with HgX(2) (X = Cl, I, SCN) is also dependent on the reaction conditions and the nature of X, two different types of adducts being formed [HgX(L)] (14: L = L(1), 16, 17: L = L(1) or L(2), X = I, 19: L = L(2), X = SCN) and [HgX(L)(2)] (15: L = L(2), X = Cl, 18: L = L(1), X = SCN). The X-ray diffraction analyses of compounds 1, 2, 4, 5, 7, 8, 10-12, 14, 15, and 19 are also reported. The variations of the coordination geometry parameters in the complexes are compared and discussed.

The Preparation, Characterization, X-ray Structural Analysis, and Thermogravimetric Analysis of Tetrakis[1,3-Dimethyl-2(3H)-Imidazolethione]Zinc(II) Nitrate and Tetrafluoroborate

Two new compounds, [Zn(dmit)4][BF4]2 and [Zn(dmit)4][NO3]2, have been synthesized and characterized via standard solid and solution state methods including single crystal X-ray crystallography (dmit = 1,3-dimethyl-2(3H)-imidazolethione). [Zn(dmit)4][BF4]2 crystallizes in space group Pbcn with a = 11.954(2) A, b = 21.260(4) A, c = 12.749(3) A, Z = 4. [Zn(dmit)4][NO3]2 crystallizes in space group I 4 1 /a with a = b = 11.091(4) A, c = 22.713(5) A, Z = 4. Both structures display a compressed tetrahedral geometry in the zinc coordination sphere similar to previously reported isopropyl and n-butyl analogs. The degree of distortion is closer to that noted for the recently reported methyl isopropyl analog than to the methyl n-butyl complex. There are no significant differences between the nitrate and tetrafluoroborate coordination spheres, and the source of distortion appears to be close intramolecular contacts. Thermogravimetric analysis results suggest that both complexes decompose to yield ZnS2 instead of ZnS. A two new ionic complexes of 1,3-dmethyl-2(3H)-imidazolethione (dmit) containing tetra-S-coordinated Zn(II) have been synthesized and structurally characterized. Both nitrate and tetrafluoroborate analogs have distorted tetrahedral coordination geometry around the zinc ions similar to that noted for complexes with bulkier alkyl imidazolethiones. There are no significant differences between the nitrate and tetrafluoroborate coordination spheres, and the source of distortion appears to be close intramolecular contacts.

Synthesis and structural diversity of oligosilanylzinc compounds

Reactions of potassium oligosilanyls with ZnCl(2) lead to the formation of oligosilanylzinc compounds with zinc's coordination sphere expanded by ligation of TMEDA, an additional oligosilanyl group, or a chloride ion.

Zinc finger proteins as templates for metal ion exchange: Substitution effects on the C-finger of HIV nucleocapsid NCp7 using M(chelate) species (M = Pt, Pd, Au)

The interactions of monofunctional [MCl(chelate)] compounds (M=Pt(II), Pd(II) or Au(III) and chelate=diethylenetriamine, dien or 2,2',2''-terpyridine, terpy) with the C-terminal finger of the HIV nucleocapsid NCp7 zinc finger (ZF) were studied by mass spectrometry and circular dichroism spectroscopy. In the case of [M(dien)] species, Pt(II) and Pd(II) behaved in a similar fashion with evidence of adducts caused by displacement of Pt-Cl or Pd-Cl by zinc-bound thiolate. Labilization, presumably under the influence of the strong trans influence of thiolate, resulted in loss of ligand (dien) as well as zinc ejection and formation of species with only Pd(II) or Pt(II) bound to the finger. For both Au(III) compounds the reactions were very fast and only "gold fingers" with no ancillary ligands were observed. For all terpyridine compounds ligand scrambling and metal exchange occurred with formation of [Zn(terpy)](2+). The results conform well to those proposed from the study of model Zn compounds such as N,N'-bis(2-mercapto-ethyl)-1,4-diazacycloheptanezinc(II), [Zn(bme-dach)](2). The possible structures of the adducts formed are discussed and, for Pt(II) and Pd(II), the evidence for possible expansion of the zinc coordination sphere from four- to five-coordinate is discussed. This observation reinforces the possibility of change in geometry for zinc in biology, even in common "structural" sites in metalloenzymes. The results further show that the extent and rate of zinc displacement by inorganic compounds can be modulated by the nature (metal, ligands) of the reacting compound.

Synthesis and structural diversity of 2-pyridylmethylideneamine complexes of zinc(II) chloride

The addition reactions of zinc(II) chloride to N-substituted pyridine-2-carbaldimines [Py–CH NR, R = Me ( 1a), Ph ( 1b), Bz ( 1c), allyl ( 1d)] lead to different complexes dependent on the N-bound substituent R. The 1:1 complexes show molecular structures of the type [(Py–CH NR)ZnCl 2] for R = methyl ( 2a), phenyl ( 2b), and allyl ( 2d) with a distorted tetrahedral environment for the zinc atom. The zinc complex with the N-methylated pyridine-2-carbaldimine also forms a dimer of the type [(Py–CH NR)ZnCl 2] 2 ( 2a) 2 with a square pyramidal coordination sphere of zinc. A 3:2 stoichiometry is observed for R = benzyl and an ion pair of the type [Zn(Py–CH NR) 3] 2+ [ZnCl 4] 2− ( 2c) is found in the solid state.

Catalytic Domain Architecture of Metzincin Metalloproteases

Metalloproteases cleave proteins and peptides, and deregulation of their function leads to pathology. An understanding of their structure and mechanisms of action is necessary to the development of strategies for their regulation. Among metallopeptidases are the metzincins, which are mostly multidomain proteins with approximately 130-260-residue globular catalytic domains showing a common core architecture characterized by a long zinc-binding consensus motif, HEXXHXXGXX(H/D), and a methionine-containing Met-turn. Metzincins participate in unspecific protein degradation such as digestion of intake proteins and tissue development, maintenance, and remodeling, but they are also involved in highly specific cleavage events to activate or inactivate themselves or other (pro)enzymes and bioactive peptides. Metzincins are subdivided into families, and seven such families have been analyzed at the structural level: the astacins, ADAMs/adamalysins/reprolysins, serralysins, matrix metalloproteinases, snapalysins, leishmanolysins, and pappalysins. These families are reviewed from a structural point of view.

The structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains

The recent characterization of the prokaryotic Cys(2)His(2) zinc-finger domain, identified in Ros protein from Agrobacterium tumefaciens, has demonstrated that, although possessing a similar zinc coordination sphere, this domain is structurally very different from its eukaryotic counterpart. A search in the databases has identified approximately 300 homologues with a high sequence identity to the Ros protein, including the amino acids that form the extensive hydrophobic core in Ros. Surprisingly, the Cys(2)His(2) zinc coordination sphere is generally poorly conserved in the Ros homologues, raising the question of whether the zinc ion is always preserved in these proteins. Here, we present a functional and structural study of a point mutant of Ros protein, Ros(56-142)C82D, in which the second coordinating cysteine is replaced by an aspartate, 5 previously-uncharacterized representative Ros homologues from Mesorhizobium loti, and 2 mutants of the homologues. Our results indicate that the prokaryotic zinc-finger domain, which in Ros protein tetrahedrally coordinates Zn(II) through the typical Cys(2)His(2) coordination, in Ros homologues can either exploit a CysAspHis(2) coordination sphere, previously never described in DNA binding zinc finger domains to our knowledge, or lose the metal, while still preserving the DNA-binding activity. We demonstrate that this class of prokaryotic zinc-finger domains is structurally very adaptable, and surprisingly single mutations can transform a zinc-binding domain into a nonzinc-binding domain and vice versa, without affecting the DNA-binding ability. In light of our findings an evolutionary link between the prokaryotic and eukaryotic zinc-finger domains, based on bacteria-to-eukaryota horizontal gene transfer, is discussed.

The Zinc proteome: a tale of stability and functionality

Zinc proteins constitute a very important portion of the large number of Metalloproteins currently known. However, contrary to what happens with biological systems containing Fe(II), Fe(III), Cu(II), Mn(II), Mn(III), Ni(II), Co(III) or other commonly found biologically relevant metal cofactors, the particular chemical properties of the Zn(II) ion mean that only a very small number of experimental techniques can be directly applied in the study of the metal coordination spheres present in Zinc proteins. The information obtainable from publicly available structural databases such as the Protein Data Bank can therefore be of particularly high significance to a better understanding of these proteins. In this study, we draw a detailed statistical portrait of the Zinc proteome by analysing the metal coordination spheres of the large number of X-ray crystallographic structures of Zinc proteins currently available on the Protein Data Bank. This data is further complemented with quantum mechanical calculations on the most common Zinc coordination spheres to evaluate the intrinsic thermodynamic stability of the several combinations of ligands on a generic and non-specific enzymatic environment, and with molecular electrostatic potential maps. These results provide useful insights into this difficult to characterize but very important Zn-containing subset of the proteome.

Molecular dynamics analysis of farnesyltransferase: A closer look into the amino acid behavior

AbstractFarnesyltransferase (FTase) is a zinc enzyme that catalyzes the addition of a 15 carbons isoprenoid group from farnesyl diphosphate to protein substrates containing a typical ‐CAAX motif, where C is a cysteine residue. Among the possible CAAX substrates for FTase are a large number of biologically relevant proteins involved in cancer development, including the Ras family of proteins. FTase thus quickly became a very promising target for anticancer therapy, despite the fact that a number of questions regarding its catalytic activity have remained unexplained. This study describes the successful application of three sets of molecular dynamics parameters specifically designed to allow a reliable treatment of the zinc coordination sphere in the four key intermediate states formed during the catalytic cycle of this enzyme—FTase resting state, binary complex (FTase‐FPP), ternary complex (FTase‐FPP‐CAAX), and product complex—allowing a detailed analysis of the dynamic behavior of the several amino acid residues that constitute the enzyme, and complementing the more rigid time‐averaged snapshot‐view given by the available X‐crystallographic structures with a more global structural vision that takes motion into account. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Mechanism of Auxin Interaction with Auxin Binding Protein (ABP1): A Molecular Dynamics Simulation Study

Auxin Binding Protein 1 (ABP1) is ubiquitous in green plants. It binds the phytohormone auxin with high specificity and affinity, but its role in auxin-induced processes is unknown. To understand the proposed receptor function of ABP1 we carried out a detailed molecular modeling study. Molecular dynamics simulations showed that ABP1 can adopt two conformations differing primarily in the position of the C-terminus and that one of them is stabilized by auxin binding. This is in agreement with experimental evidence that auxin induces changes at the ABP1 C-terminus. Simulations of ligand egress from ABP1 revealed three main routes by which an auxin molecule can enter or leave the ABP1 binding site. Assuming the previously proposed orientation of ABP1 to plant cell membranes, one of the routes leads to the membrane and the other two to ABP1's aqueous surroundings. A network of hydrogen-bonded water molecules leading from the bulk water to the zinc-coordinated ligands in the ABP1 binding site was formed in all simulations. Water entrance into the zinc coordination sphere occurred simultaneously with auxin egress. These results suggest that the hydrogen-bonded water molecules may assist in protonation and deprotonation of auxin molecules and their egress from the ABP1 binding site.

Analysis of zinc‐ligand bond lengths in metalloproteins: Trends and patterns

Zinc is one of the biologically most abundant and important metal elements, present in a plethora of enzymes from a broad array of species of all phyla. In this study we report a thorough analysis of the geometrical properties of Zinc coordination spheres performed on a dataset of 994 high quality protein crystal structures from the Protein Data Bank, and complemented with Quantum mechanical calculations at the DFT level of theory (B3LYP/SDD) on mononuclear model systems. The results allowed us to draw interesting conclusions on the structural characteristics of Zn centres and to evaluate the importance of such effects as the resolution of X-ray crystallographic structures, the enzyme class in which the Zn centre is included, and the identity of the ligands at the Zn coordination sphere. Altogether, the set of results obtained provides useful data for the enhancement of the atomic models normally applied to the theoretical and computational study of zinc enzymes at the quantum mechanical level (in particular enzymatic mechanisms), and for the development of molecular mechanical parameters for the treatment of zinc coordination spheres with molecular mechanics or molecular dynamics in studies with the full enzyme.

Theoretical studies on farnesyltransferase: The distances paradox explained

In spite of the enormous interest that has been devoted to its study, the mechanism of the enzyme farnesyltransferase (FTase) remains the subject of several crucial doubts. In this article, we shed a new light in one of the most fundamental dilemmas that characterize the mechanism of this puzzling enzyme commonly referred to as the "distances paradox", which arises from the existence of a large 8-A distance between the two reactive atoms in the reaction catalyzed by this enzyme: a Zn-bound cysteine sulphur atom from a peptidic substrate and the farnesyldiphosphate (FPP) carbon 1. This distance must be overcome for the reaction to occur. In this study, the two possible alternatives were evaluated by combining molecular mechanics (AMBER) and quantum chemical calculations (B3LYP). Basically, our results have shown that an activation of the Zn-bound cysteine thiolate with subsequent displacement from the zinc coordination sphere towards the FPP carbon 1 is not a realistic hypothesis of overcoming the large distance reported in the crystallographic structures of the ternary complexes between the two reactive atoms, but that a rotation involving the FPP molecule can bring the two atoms closer with moderate energetic cost, coherent with previous experimental data. This conclusion opens the door to an understanding of the chemical step in the farnesylation reaction.

Cys xHis y–Zn 2+ interactions: Possibilities and limitations of a simple pairwise force field

In zinc proteins, the Zn 2+ cation frequently binds with a tetrahedral coordination to cysteine and histidine side chains. We examine the possibilities and limitations of a classical, pairwise force field for molecular dynamics of such systems. Hartree Fock and density functional calculations are used to obtain geometries, charge distributions, and association energies of side chain analogues bound to Zn 2+. Both ionized and neutral cysteines are considered. Two parameterizations are obtained, then tested and compared through molecular dynamics simulations of two small, homologous proteins in explicit solvent: Protein Kinase C and the Cysteine Rich Domain (CRD) of Raf, which have two Cys 3His–Zn 2+ groups each. The lack of explicit polarizability and charge transfer in the force field leads to poor accuracy for the association energies, and to parameters—including the zinc charge, that depend on the number of bound cysteines and their protonation state. Nevertheless, the structures sampled with the best parameterization are in good overall agreement with experiment, and have zinc coordination geometries compatible with related structures in the Cambridge Structural Database and the Protein Data Bank. Non-optimized parameters lead to poorer structures. This suggests that while a simple force field is not appropriate for processes involving exchange between water and amino acids in the zinc coordination sphere (e.g. protein unfolding), it can be useful for equilibrium simulations of stable Cys 3His zinc fingers.