Theoretical Appraisal of Cyclopropenone: Aggregation and Complexes with Water.

Cyclopropenone (HCCOCH, "CPN") is an exotic quasi-aromatic cyclic carbene that abounds in the interstellar medium (ISM). Astronomical observations suggest that (i) stagnate CPN exhibits a tendency to polymerize and that (ii) interactions may occur between CPN and water that is also ubiquitous in the ISM. In this light, density functional theory investigations reveal cooperative hydrogen bonding, which leads to stable polymeric conformations of (CPN)n, tracked up to n = 14. Stable agglomerations with water, however, constitute at best only two CPN and two water molecules, signifying that while CPN exhibits remarkable cooperativity for "cohesive" clustering via hydrogen bonding, this tendency is markedly diminished for "hetero"-interactions. Multifaceted data are employed to probe cogent molecular descriptors, such as structure and energetics of various conformers, vibrational spectroscopic response, molecular electrostatic potential (MESP), effective atomic charges: all these, in unison, describe the evolution of the characteristics upon cluster formation. Salient stretching frequency shifts, as well as charge redistribution gleaned from MESP morphology, have a direct bearing on variegated hydrogen bonding patterns: linear, nonlinear, as well as bifurcated. In particular, characteristic C-H, C═O stretching, and O-H vibrations in the water complexes reveal a "softening" (downshift) of frequencies. While small conformers have markedly distinct MESP variations, the differences become less pronounced with incremental clustering, an effect substantiated by corresponding emergent atomic charges.

Mechanistic Investigation of Site-specific DNA Methylating Agents Targeting Breast Cancer Cells.

We previously described the development of a DNA-alkylating compound that showed selective toxicity in breast cancer cells. This compound contained an estrogen receptor α (ERα)-binding ligand and a DNA-binding/methylating component that could selectively methylate the N3-position of adenines at adenine-thymine rich regions of DNA. Herein, we describe mechanistic investigations that demonstrate that this class of compounds facilitate the translocation of the ERα-compound complex to the nucleus and induce the expression of ERα target genes. We confirm that the compounds show selective toxicity in ERα-expressing cells, induce ERα localization in the nucleus, and verify the essential role of ERα in modulating the toxicity. Minor alterations in the compound structure significantly affects the DNA binding ability, which correlates to the DNA-methylating ability. These studies demonstrate the utility of DNA-alkylating compounds to accomplish targeted inhibition of the growth of specific cancer cells; an approach that may overcome shortcomings of currently used chemotherapy agents.

Impact of Local Electrostatics on the Redox Properties of Tryptophan Radicals in Azurin: Implications for Redox-Active Tryptophans in Proton-Coupled Electron Transfer.

Tyrosine and tryptophan play critical roles in facilitating proton-coupled electron transfer (PCET) processes essential to life. The local protein environment is anticipated to modulate the thermodynamics of amino acid radicals to achieve controlled, unidirectional PCET. Herein, square-wave voltammetry was employed to investigate the electrostatic effects on the redox properties of tryptophan in two variants of the protein azurin. Each variant contains a single redox-active tryptophan, W48 or W108, in a unique and buried protein environment. These tryptophan residues exhibit reversible square-wave voltammograms. A Pourbaix plot, representing the reduction potentials versus pH, is presented for the non-H-bonded W48, which has potentials comparable to those of tryptophan in solution. The reduction potentials of W108 are seen to be increased by more than 100 mV across the same pH range. Molecular dynamics shows that, despite its buried indole ring, the N-H of W108 hydrogen bonds with a water cluster, while W48 is completely excluded from interactions with water or polar groups. These redox properties provide insight into the role of the protein in tuning the reactivity of tryptophan radicals, a requirement for controlled biological PCET.

Multigenerational Theoretical Study of Isoprene Peroxy Radical 1-5-Hydrogen Shift Reactions that Regenerate HO x Radicals and Produce Highly Oxidized Molecules.

A computational protocol is employed to glean new insight into the kinetics of several 1,5-hydrogen atom (H) shift reactions subsequent to first- and second-generation OH/O2 additions to isoprene. The M06-2X density functional was initially used with the Nudged Elastic Band (NEB) method to determine the potential energy surface of OH/O2 addition reactions, the 1,5-H shift reactions, and the fragmentation exit channels. The Master Equation Solver for Multi-Energy Well Reactions (MESMER) was applied to determine the rate constants for OH addition and the 1,5-H shifts. M06-2X was capable of quantifying the rate constants of OH addition to the first and second double bonds of isoprene with deviations less than 17% from the experimentally determined values. However, M06-2X underestimated the 1,5-H shift rate constants of second-generation isoprene peroxy radicals. Consequently, MN15, ωB97X-D, and CBS-QB3 methods were employed to compute average barrier heights to first- and second-generation 1,5-H shifts. In the first generation, the rate constants of H abstraction by ß-(1,2) and (4,3) isoprene hydroxy-peroxy radicals from the neighboring hydroxyl group are 1.1 × 10-3 and 2.4 × 10-3 s-1, respectively. These values are determined primarily by the barrier of the H shift reaction and, to a smaller albeit nonnegligible extent, by the stability of the resulting alkoxy radical and the exit barrier leading to C-C bond dissociation. In contrast, the average second-generation rate constant of 1,5-H shifts from H-R-OH sites to the peroxy radical is 1.8 × 10-1 s-1, with tunneling playing the significant role of increasing this value relative to first-generation 1,5-H shifts. Under low NO x conditions, first-generation isoprene oxidation reactions may recycle HO x at levels ranging from 10 to 30% due in large part to 1,5-H shifts, with the recycling efficiency being sensitive to HO2 concentrations and temperature. HO x recycling is expected to increase to levels beyond 80% in second-generation reactions of oxidized isoprene species because of isoprene epoxydiol (IEPOX) formation and further 1,5-H shifts that are kinetically favorable.

Harmonizing accuracy and efficiency: A pragmatic approach to fragmentation of large molecules.

Fragmentation methods offer an attractive alternative for ab initio treatment of large molecules and molecular clusters. However, balancing the accuracy and efficiency of these methods is a tight-rope-act. With this in view, we present an algorithm for automatic molecular fragmentation within Molecular Tailoring Approach (MTA) achieving this delicate balance. The automated code is tested out on a variety of molecules and clusters at the Hartree-Fock (HF)- and Møller-Plesset second order perturbation theory as well as density functional theory employing augmented Dunning basis sets. The results show remarkable accuracy and efficiency vis-à-vis the respective full calculations. Thus the present work forms an important step toward the development of an MTA-based black box code for implementation of HF as well as correlated quantum chemical calculations on large molecular systems.

Noncovalent interactions underlying binary mixtures of amino acid based ionic liquids: insights from theory.

Mixtures of ionic liquids formed by blending a common 1-methyl-3-butylimidazolium [Bmim] cation with the dicarboxylic amino acid anions viz., aspartic acid [Asp], asparagine [Asn], glutamic acid [Glu], and glutamine [Gln], have been investigated by employing dispersion corrected density functional theory. Binary mixtures of [Bmim]2[Asp][Asn] and [Bmim]2[Glu][Gln] ionic liquids emerge with distinct structural patterns. Competition between the constituting anions towards cationic binding sites in acidic and basic (polar) amino acid binary mixtures engenders diverse noncovalent interactions, viz., C-HO hydrogen bonding, π-π stacking, and lpπ and CHπ interactions, which impart local liquid structure to these systems governing the structural and physicochemical properties of such double salt ionic liquids (DSILs). The DSIL conformers reveal distinct structural features arising from the middle, normal and front arrangements of anions combined with parallel, antiparallel, rotated or displaced orientations of the cations. The inclusion of dispersion corrections through the D3 method affects their binding energies significantly bringing forth alteration in their energy rank order. Molecular insights accompanying the ion aggregates provide directives for the use of DSILs with improved performance in tribological applications.

Barrierless Reactions with Loose Transition States Govern the Yields and Lifetimes of Organic Nitrates Derived from Isoprene.

The chemical reaction mechanism of NO addition to two ß and δ isoprene hydroxy-peroxy radical isomers is examined in detail using density functional theory, coupled cluster methods, and the energy resolved master equation formalism to provide estimates of rate constants and organic nitrate yields. At the M06-2x/aug-cc-pVTZ level, the potential energy surfaces of NO reacting with ß-(1,2)-HO-IsopOO• and δ-Z-(1,4)-HO-IsopOO• possess barrierless reactions that produce alkoxy radicals/NO2 and organic nitrates. The nudged elastic band method was used to discover a loosely bound van der Waals (vdW) complex between NO2 and the alkoxy radical that is present in both exit reaction channels. Semiempirical master equation calculations show that the ß organic nitrate yield is 8.5 ± 3.7%. Additionally, a relatively low barrier to C-C bond scission was discovered in the ß-vdW complex that leads to direct HONO formation in the gas phase with a yield of 3.1 ± 1.3%. The δ isomer produces a looser vdW complex with a smaller dissociation barrier and a larger isomerization barrier, giving a 2.4 ± 0.8% organic nitrate yield that is relatively pressure and temperature insensitive. By considering all of these pathways, the first-generation NOx recycling efficiency from isoprene organic nitrates is estimated to be 21% and is expected to increase with decreasing NOx concentration.

Glycoconjugated Site-Selective DNA-Methylating Agent Targeting Glucose Transporters on Glioma Cells.

DNA-alkylating drugs continue to remain an important weapon in the arsenal against cancers. However, they typically suffer from several shortcomings because of the indiscriminate DNA damage that they cause and their inability to specifically target cancer cells. We have developed a strategy for overcoming the deficiencies in current DNA-alkylating chemotherapy drugs by designing a site-specific DNA-methylating agent that can target cancer cells because of its selective uptake via glucose transporters, which are overexpressed in most cancers. The design features of the molecule, its synthesis, its reactivity with DNA, and its toxicity in human glioblastoma cells are reported here. In this molecule, a glucosamine unit, which can facilitate uptake via glucose transporters, is conjugated to one end of a bispyrrole triamide unit, which is known to bind to the minor groove of DNA at A/T-rich regions. A methyl sulfonate moiety is tethered to the other end of the bispyrrole unit to serve as a DNA-methylating agent. This molecule produces exclusively N3-methyladenine adducts upon reaction with DNA and is an order of magnitude more toxic to treatment resistant human glioblastoma cells than streptozotocin is, a Food and Drug Administration-approved, glycoconjugated DNA-methylating drug. Cellular uptake studies using a fluorescent analogue of our molecule provide evidence of uptake via glucose transporters and localization within the nucleus of cells. These results demonstrate the feasibility of our strategy for developing more potent anticancer chemotherapeutics, while minimizing common side effects resulting from off-target damage.

Probing Molecular Interactions in Functionalized Asymmetric Quaternary Ammonium-Based Dicationic Ionic Liquids.

Electronic structure, binding energies, and spectral characteristics of functionalized asymmetric dicationic ionic liquids (DILs) composed of quaternary ammonium cations substituted with the ethoxyethyl and allyl/3-phenylpropyl/methoxyethoxyethyl/pentyl functionalities on two different nitrogen centers of the dication and the bis(trifluoromethanesulfonyl)imide (Tf2N-) anion were derived employing the dispersion-corrected density functional theory. DILs based on methoxyethoxyethyl-substituted cation reveal stronger binding toward the Tf2N- anion. The measured glass transition temperatures are found to be strongly dependent on the cation-anion binding facilitated through noncovalent interactions with dominant contributions from the electrostatics and hydrogen bonding. The manifestations of these interactions to vibrational spectra, in particular, to SO2 and CF3 stretchings in the complexes are presented. It has been demonstrated that the frequency down (red)-shift of the SO2 stretching in these DILs with varying substituent follows the order: methoxyethoxyethyl (35 cm-1) > allyl (23 cm-1) > pentyl (20 cm-1) > 3-phenylpropyl (5 cm-1), which is consistent with the strength of cation-anion binding. The CF3 stretching of the anion exhibits the frequency shift in the opposite direction with its hierarchy being reversed to that of SO2 stretchings; the largest upshift (blue shift) of 60 cm-1 was predicted for the DILs composed of 3-phenlpropyl substituted dications. The direction of such frequency shift has been rationalized through the difference molecular electron density maps in conjunction with the electron density at the bond critical point in the quantum theory of atoms in molecules. The underlying cation-anion binding has been analyzed through charge distribution analysis characterized in terms of molecular electrostatic potential topography. Furthermore, the observed decomposition temperatures of DILs are shown to correlate well with the maximum surface electrostatic potential parameters in quantum theory of atoms in molecules.

Encaged molecules in external electric fields: A molecular "tug-of-war".

Response of polar molecules CH3OH and H2O2 and a non-polar molecule, CO2, as "guests" encapsulated in the dodecahedral water cage (H2O)20 "host," to an external, perturbative electric field is investigated theoretically. We employ the hybrid density-functionals M06-2X and ωB97X-D incorporating the effects of damped dispersion, in conjunction with the maug-cc-pVTZ basis set, amenable for a hydrogen bonding description. While the host cluster (cage) tends to confine the embedded guest molecule through cooperative hydrogen bonding, the applied electric field tends to rupture the cluster-composite by stretching it; these two competitive effects leading to a molecular "tug-of-war." The composite remains stable up to a maximal sustainable threshold electric field, beyond which, concomitant with the vanishing of the HOMO-LUMO gap, the field wins over and the cluster breaks down. The electric-field effects are gauged in terms of the changes in the molecular geometry of the confined species, interaction energy, molecular electrostatic potential surfaces, and frequency shifts of characteristic normal vibrations in the IR regime. Interestingly, beyond the characteristic threshold electric field, the labile, distorted host cluster fragmentizes, and the guest molecule still tethered to a remnant fragment, an effect attributed to the underlying hydrogen-bonded networks.

The N-terminal of annexin A1 as a secondary membrane binding site: a molecular dynamics study.

Annexin A1 has been shown to cause membrane aggregation and fusion, yet the mechanism of these activities is not clearly understood. In this work, molecular dynamics simulations were performed on monomeric annexin A1 positioned between two negatively charged monolayers using AMBER's all atom force field to gain insight into the mechanism of fusion. Each phospolipid monolayer was made up of 180 DOPC molecules and 45 DOPG molecules to achieve a 4:1 ratio. The space between the two monolayers was explicitly solvated using TIP3P waters in a rectilinear box. The constructed setup contained up to 0.14 million atoms. Application of periodic boundary conditions to the simulation setup gave the desired effect of two continuous membrane bilayers. Nonbonded interactions were calculated between the N-terminal residues and the bottom layer of phospholipids, which displayed a strong attraction of K26 and K29 to the lipid head-groups. The side-chains of these two residues were observed to orient themselves in close proximity (∼3.5 Å) with the polar head-groups of the phospholipids.

A computational study of acid catalyzed aerosol reactions of atmospherically relevant epoxides.

Epoxides are important intermediates of atmospheric isoprene oxidation. Their subsequent reactions in the particle phase lead to the production of organic compounds detected in ambient aerosols. We apply density functional theory to determine the important kinetic factors that drive epoxide reactions in the particle phase. Specifically, the importance of acid catalysis and solvent polarity are investigated using a variety of epoxides and nucleophiles. The condensed phase is modeled using molecular clusters immersed in a dielectric continuum and a majority of the calculations are performed with the M062x density functional and the 6-311++G** basis set. Calculations of acid catalyzed epoxide hydrolysis transition states for simple primary, secondary and tertiary epoxides are consistent with an A-2 mechanism where the nucleophile (water) interacts with an epoxide carbon in the transition state. By applying transition state theory to this mechanism, the overall rate constants of epoxide reactions such as hydrolysis, organosulfate formation, organonitrate formation and oligomerization are determined. The calculations indicate that the acid catalyzed hydrolysis rate constant of 2-methyl-2,3-epoxybutane-1,4-diol (ß-IEPOX--an isoprene epoxide produced under low NOx conditions) is approximately 30 times greater than 2-methyl-2,3-epoxypropanoic acid (MAE--methacrylic acid epoxide derived from isoprene and produced at high NOx concentrations). Furthermore, acid catalyzed organosulfate formation and epoxide oligomerization reactions are competitive and appear to be kinetically favorable over the hydrolysis of IEPOX.

Epoxide as a precursor to secondary organic aerosol formation from isoprene photooxidation in the presence of nitrogen oxides.

Isoprene is a substantial contributor to the global secondary organic aerosol (SOA) burden, with implications for public health and the climate system. The mechanism by which isoprene-derived SOA is formed and the influence of environmental conditions, however, remain unclear. We present evidence from controlled smog chamber experiments and field measurements that in the presence of high levels of nitrogen oxides (NO(x) = NO + NO2) typical of urban atmospheres, 2-methyloxirane-2-carboxylic acid (methacrylic acid epoxide, MAE) is a precursor to known isoprene-derived SOA tracers, and ultimately to SOA. We propose that MAE arises from decomposition of the OH adduct of methacryloylperoxynitrate (MPAN). This hypothesis is supported by the similarity of SOA constituents derived from MAE to those from photooxidation of isoprene, methacrolein, and MPAN under high-NOx conditions. Strong support is further derived from computational chemistry calculations and Community Multiscale Air Quality model simulations, yielding predictions consistent with field observations. Field measurements taken in Chapel Hill, North Carolina, considered along with the modeling results indicate the atmospheric significance and relevance of MAE chemistry across the United States, especially in urban areas heavily impacted by isoprene emissions. Identification of MAE implies a major role of atmospheric epoxides in forming SOA from isoprene photooxidation. Updating current atmospheric modeling frameworks with MAE chemistry could improve the way that SOA has been attributed to isoprene based on ambient tracer measurements, and lead to SOA parameterizations that better capture the dependency of yield on NO(x).

Exploring electric field induced structural evolution of water clusters, (H2O)n [n = 9-20]: density functional approach.

Response of neutral water clusters (H(2)O)(n), n = 9-20, to external uniform dipolar static electric fields is studied for some lowest-energy conformers for each "n" within an energy band of about 9 kcal mol(-1) of their field-free counterparts. We perform density functional theory computations with B3LYP∕6-311++G(2d,2p) model chemistry. Increasing the electric field destabilizes and distorts a cluster by elongating, hence weakening its hydrogen bonds, culminating into a catastrophic structural breakdown beyond a specific threshold field-strength. The electric field induced conformational transitions to extended structures stretched along the field direction to lower-energy configurations that appear as local minima on their potential energy surface are presented. It is observed that a typical structural transition of this type is always accompanied by an abrupt increase in the electric dipole moment of the cluster over and above its smooth increment with increasing applied field; the increase being phenomenal during breakdown. Interestingly, the HOMO-LUMO energy gap for a given conformer is found to diminish with increasing field strength, abruptly approaching zero at structural breakdown. In essence, the structural evolution traced through hydrogen-bond networks of the clusters reveals multiple enhancements in size by "opening up" of three-dimensional morphologies to form net-like structures with less number of hydrogen bonds. These clusters exhibit greater structural complexity than that encountered in the relatively small clusters reported previously.

Intramolecular hydrogen bond energy and cooperative interactions in α-, ß-, and γ-cyclodextrin conformers.

Accurate estimation of individual intramolecular hydrogen bond (H-bond) energies is an intricate task for multiply H-bonded systems. In such cases, the hydrogen bond strengths could be highly influenced by the cooperative interactions, for example, those between hydroxyl groups in sugars. In this work, we use the recently proposed molecular tailoring approach-based quantification (Deshmukh, Gadre, and Bartolotti, J Phys Chem A 2006, 110, 12519) to the extended systems of cyclodextrins (CDs). Further, the structure and stability of different conformers of α-, ß-, and γ-CDs are explained based on the energetics and cooperative contribution to the strength of these H-bonds. The estimated O-H···O H-bond energies in the various CD conformers are found to vary widely from 1.1 to 8.3 kcal mol(-1). The calculated energy contributions to cooperativity toward the H-bond strengths fall in the range of 0.25-2.75 kcal mol(-1).

Microsolvation of methyl hydrogen peroxide: ab initio quantum chemical approach.

Methyl hydrogen peroxide (MHP), one of the simplest organic hydroperoxides, is a strong oxidant, with enhanced activity in aqueous ambience. The present study investigates, at the molecular level, the role of hydrogen bonding that is conducive to cluster formation of MHP with water molecules from its peroxide end, with the methyl group remaining hydrophobic for up to five water molecules. Ab initio quantum chemical computations on MHP...(H(2)O)(n), [n=1-5] are performed at second order Møller-Plesset (MP2) perturbation theory employing the basis sets 6-31G(d,p) and 6-311++G(2d,2p) to study the cluster formation of MHP with water molecules from its peroxide end and hydrophobic hydration due to the methyl group. Successive addition of water molecules alters the hydrogen bonding pattern, which leads to changes in overall cluster geometry and in turn to IR vibrational frequency shifts. Molecular co-operativity in these clusters is gauged directly through a detailed many-body interaction energy analysis. Molecular electrostatic potential maps are shown to have a bearing on predicting further growth of these clusters, which is duly corroborated through sample calculations for MHP...(H(2)O)(8). Further, a continuum solvation model calculation for energetically stable clusters suggests that this study should serve as a precursor for pathways to aqueous solvation of MHP.

Computational screening and design of S100B ligand to block S100B-p53 interaction.

The binding of S100B to p53 disables the biological function of p53 as a tumor suppressor and thus causes cancer. It is very important to explore the interaction between S100B and p53 and to develop inhibitors to block the interaction in anti-cancer development. In this work, the interaction of S100B to p53 was studied using molecular dynamics (MD) at the atomic level and organic molecules have been identified as potential inhibitors to block the S100B-p53 interaction. It was indicated in the simulations that S100B residues around GLU45 and GLU46 play an important role in the binding of S100B to p53. The three dimensional structure of S100B obtained from S100B-p53 complex (PDB ID: 1DT7) was used as the target protein receptor. Multiple LUDI screenings for S100B ligands were performed using different searching radii 6.23 A, 7.23 A, 8.23 A, 9.23 A and 10.23A with a searching center which was defined as the geometrical center of S100B residues that are within 5A from the p53 C-terminal peptide in the complex. Potential organic compounds were screened from the ZINC database using LUDI program implemented in Cerius2 package and evaluated as potential S100B ligands to block the S100B-p53 interaction. The top-scored compounds were selected for binding affinity calculation. The results show that these top-scored ZINC compounds bind in the location where p53 binds and interact with S100B in a similar fashion as p53, and therefore it is expected that they have the potential to block S100B from binding to p53. The ADME and toxicity properties of the potential S100B ligands were also evaluated.

Molecular dynamics simulation studies on Ca2+ -induced conformational changes of annexin I.

Cryo-electron microscopy (EM) and X-ray studies proposed different mechanisms for annexin-induced membrane aggregation. In this work, molecular dynamics (MD) simulation technique was utilized to gain an insight into the calcium-induced conformational changes on annexin I and their implication in membrane aggregation mechanism. MD simulations were performed on the Ca2+ -free annexin I with the N-terminal domain buried inside the core (System 1), the Ca2+ -bound annexin I without N-terminal domain (System 2) and the Ca2+ -bound annexin I with the N-terminal domain exposed (System 3). Our results indicated that calcium binding increases the flexibility of annexin I core domain residues including the calcium coordinating residues. As a result, annexin I was activated to interact with the negatively charged membrane. The exposed N-terminal domain was very flexible and gradually lost the secondary structure during MD simulation, suggesting that the N-terminal may adopt a favorable conformation to bind a second membrane and also explaining the failure of attempts to crystallize the full-length annexin I in the presence of calcium ions. The measured dimensions of the averaged simulation structure of the Ca2+ -bound annexin I with the N-terminal exposed (System 3) support the proposed membrane aggregation mechanism based on X-ray studies.

Intramolecular hydrogen bonding and cooperative interactions in carbohydrates via the molecular tailoring approach.

In spite of many theoretical and experimental attempts for understanding intramolecular hydrogen bonding (H-bonding) in carbohydrates, a direct quantification of individual intramolecular H-bond energies and the cooperativity among the H-bonded networks has not been reported in the literature. The present work attempts, for the first time, a direct estimation of individual intramolecular O-H...O interaction energies in sugar molecules using the recently developed molecular tailoring approach (MTA). The estimated H-bond energies are in the range of 1.2-4.1 kcal mol(-1). It is seen that the OH...O equatorial-equatorial interaction energies lie between 1.8 and 2.5 kcal mol(-1), with axial-equatorial ones being stronger (2.0-3.5 kcal mol(-1)). The strongest bonds are nonvicinal axial-axial H-bonds (3.0-4.1 kcal mol(-1)). This trend in H-bond energies is in agreement with the earlier reports based on the water-water H-bond angle, solvent-accessible surface area (SASA), and (1)H NMR analysis. The contribution to the H-bond energy from the cooperativity is also estimated using MTA. This contribution is seen to be typically between 0.1 and 0.6 kcal mol(-1) when H-bonds are a part of a relatively weak equatorial-equatorial H-bond network and is much higher (0.5-1.1 kcal mol(-1)) when H-bonds participate in an axial-axial H-bond network.

Copper and zinc promote interactions between membrane-anchored peptides of the metal binding domain of the prion protein.

The prion protein (PrP) has been identified as a metalloprotein capable of binding multiple copper ions and possibly zinc. Recent studies now indicate that prion self-recognition may be an important factor in both the normal function and misfunction of this protein. We have developed fluorescently labeled models of the prion protein that allow prion-prion interactions and metal binding to be investigated on the molecular level. Peptides encompassing the full metal binding region were anchored to the surface of small unilamellar vesicles, and PrP-PrP interactions were monitored by fluorescence spectroscopy as a function of added metal. Both Cu2+ and Zn2+ were found to cause an increase in the level of PrP-PrP interactions, by 117 and 300%, respectively, whereas other metals such as Ni2+, Co2+, and Ca2+ had no effect. The binding of either of these cofactors appears to act as a switch that induces PrP-PrP interactions in a reversible manner. Both glutamine and tryptophan residues, which occur frequently in the metal binding region of PrP, were found to be important in mediating PrP-PrP interactions. Experiments demonstrate that tryptophan residues are also responsible for the low level of PrP-PrP interactions observed in the absence of Cu2+ and Zn2+, and this is further supported by molecular modeling. Overall, our results indicate that PrP may be a bifunctional molecule capable of responding to fluctuations in both neuronal Cu2+ and Zn2+ levels.