Molecular-dynamics simulation of the beta domain of metallothionein with a semi-empirical treatment of the metal core

Experimental and theoretical studies of cadmium ions absorption by a new reduced recombinant defensin

Heavy metal pollutants such as Cd, Hg, Pb, As, and Se are considered as both a global problem and a growing threat to the humanity. Being strongly poisonous to the metal-sensitive enzymes and leading to the growth inhibition and death of organisms, these metals have a toxic impact on the plants and animals. Inducing the metal-binding cysteine-rich peptides such as metallothioneins, phytochelatins, and defensins, higher organisms like plants and animals usually react to the heavy metal stress. In this study, a recombinant defensin protein was expressed in bean and its ability in the cadmium absorption was determined. Experimental studies revealed that this protein was able to absorb cadmium ions in reduced form more than oxide one. Molecular dynamics simulations were carried out in order to evaluation of experimental studies, using a model of Cd²⁺ or Na⁺ and Cl^- ions enclosed in a fully hydrated simulation box with the recombinant defensin. The theoretical results also suggested that the reduced recombinant defensin was more powerful in the absorption of Cd²⁺ than its oxide form. The present study is the first report of Cd²⁺ absorption potential of this new reduced recombinant defensin. The results unraveled that this recombinant defensin can be adopted as a molecular switch in the cadmium pollution of the environment and also the important role of sulfur groups in the absorption of cadmium ions.

Selective cysteine modification of metal-free human metallothionein 1a and its isolated domain fragments: Solution structural properties revealed via ESI-MS

Human metallothionein 1a, a protein with two cysteine-rich metal-binding domains (α with 11 Cys and β with 9), was analyzed in its metal-free form by selective, covalent Cys modification coupled with ESI-MS. The modification profiles of the isolated β- and α-fragments reacted with p-benzoquinone (Bq), N-ethylmalemide (NEM) and iodoacetamide (IAM) were compared with the full length protein using ESI-mass spectral data to follow the reaction pathway. Under denaturing conditions at low pH, the reaction profile with each modifier followed pathways that resulted in stochastic, Normal distributions of species whose maxima was equal to the mol. eq. of modifier added. Our interpretation of modification at this pH is that reaction with the cysteines is unimpeded when the full protein or those of its isolated domains are denatured. At neutral pH, where the protein is expected to be folded in a more compact structure, there is a difference in the larger Bq and NEM modification, whose reaction profiles indicate a cooperative pattern. The reaction profile with IAM under native conditions follows a similar stochastic distribution as at low pH, suggesting that this modifier is small enough to access the cysteines unimpeded by the compact structure. The data emphasize the utility of residue modification coupled with electrospray ionization mass spectrometry for the study of protein structure.

A theoretical and experimental study of calcium, iron, zinc, cadmium, and sodium ions absorption by aspartame

Aspartame (L-Aspartyl-L-phenylalanine methyl ester) is a sweet dipeptide used in some foods and beverages. Experimental studies show that aspartame causes osteoporosis and some illnesses, which are similar to those of copper and calcium deficiency. This raises the issue that aspartame in food may interact with cations and excrete them from the body. This study aimed to study aspartame interaction with calcium, zinc, iron, sodium, and cadmium ions via molecular dynamics simulation (MD) and spectroscopy. Following a 480-ns molecular dynamics simulation, it became clear that the aspartame is able to sequester Fe²⁺, Ca²⁺, Cd²⁺, and Zn²⁺ ions for a long time. Complexation led to increasing UV-Vis absorption spectra and emission spectra of the complexes. This study suggests a potential risk of cationic absorption of aspartame. This study suggests that purification of cadmium-polluted water by aspartame needs a more general risk assessment.

Modeling Zn²⁺ release from metallothionein

Mammalian metallothioneins (MTs) comprise a Zn3Cys9 cluster in the β domain and a Zn4Cys11 cluster in the α domain. They play a crucial role in storing and donating Zn(2+) ions to target metalloproteins and have been implicated in several diseases, thus understanding how MTs release Zn(2+) is of widespread interest. In this work, we present a strategy to compute the free energy for releasing Zn(2+) from MTs using a combination of classical molecular dynamics (MD) simulations, quantum-mechanics/molecular-mechanics (QM/MM) minimizations, and continuum dielectric calculations. The methodology is shown to reproduce the experimental observations that (1) the Zn-binding sites do not have equal Zn(2+) affinity and (2) the isolated β domain is thermodynamically less stable and releases Zn(2+) faster with oxidizing agents than the isolated α domain. It was used to compute the free energies for Zn(2+) release from the metal cluster in the absence and presence of the protein matrix (protein architecture and coupled protein-water interactions) to yield the respective disulfide-bonded product. The results show the importance of the protein matrix as well as protein dynamics and coupled conformational changes in accounting for the differential Zn(2+)-releasing propensity of the two domains with oxidizing agents.

Metallothionein Zn2+- and Cu2+-clusters from first-principles calculations

Detailed electronic structures of Zn(II) and Cu(II) clusters from metallothioneins (MT) have been obtained using density functional theory (DFT), in order to investigate how oxidative stress-caused Cu(II) intermediates affect Zn-binding to MT and cooperatively lead to Cu(I)MT. The inferred accuracy is ∼0.02-0.03 Å for metal-thiolate bond lengths for the models that are the most realistic MT models so far studied by DFT. We find terminal Zn-S and Cu-S bond lengths of 2.35-2.38 Å and 2.30-2.34 Å, whereas bridging M-S bonds are 0.05-0.11 Å longer. This electronic effect is also reflected in changes in electron density on bridging sulfurs. Various imposed backbone constraints quantify the sensitivity of cluster electronic structure towards protein conformational changes. The large negative charge densities of the clusters are central to MT function, and the smaller β-clusters are more prone to modification. Oxidative stress-associated Cu(II) binding weakens the Zn-S bonds and is thus likely to impair the Zn(II) transfer function of MTs, providing a mechanism for cooperative Cu(II) binding leading to loss of Zn(II) and dysfunctional Cu(I)MT clusters.

Full quantum-mechanical structure of the human protein Metallothionein-2

Metallothioneins (MT) are small, metal-binding proteins with diverse functions related to metal ion homeostasis. This paper presents the full 384-388-atom structures of the two native Zn(II)- and the Cd(II)-containing domains of human MT2, optimized with density functional theory. The presented structures are accurate to ~0.03 Å for bond lengths and thus provide new physical insight into the detailed electronic structures of MTs, in particular with accurate accounts of bridging vs. terminal bonds not available from NMR or EXAFS. The MT protein enhances the asymmetry, as compared to the protein-free clusters, causing a hierarchy in binding that most likely allows MTs to transfer ions to multiple targets in vivo. The protein polarization is substantial and occurs primarily via the terminal sulfurs, a key mechanism in providing domain-specific electronic structures. The β-domain polarizes its smaller cluster less on average, due to its less polarizable, higher negative charge density, as reflected in longer MS bond lengths and smaller bond orders. This may explain why MT2β is more reactive and dynamic and why MTs have evolved two different-size, asymmetric domains with different metal binding affinities fit for different molecular targets of metal ion transfer.

Influence of NH-Sgamma bonding interactions on the structure and dynamics of metallothioneins

Mammalian metallothioneins ([Formula: see text]) show a clustered arrangement of the metal ions and a nonregular protein structure. The solution structures of Cd(3)-thiolate cluster containing beta-domain of mouse beta-MT-1 and rat beta-MT-2 show high structural similarities, but widely differing structure dynamics. Molecular dynamics simulations revealed a substantially increased number of NH-Sgamma hydrogen bonds in beta-MT-2, features likely responsible for the increased stability of the Cd(3)-thiolate cluster and the enfolding protein domain. Alterations in the NH-Sgamma hydrogen-bonding network may provide a rationale for the differences in dynamic properties encountered in the beta-domains of MT-1, -2, and -3 isoforms, believed to be essential for their different biological function.

Force fields including charge transfer and local polarization effects: Application to proteins containing multi/heavy metal ions

The question whether molecular dynamics (MD) simulations can yield reliable structural and dynamical properties of metalloproteins depend on the accuracy of the force field, i.e., the potential energy function (PEF) and associated parameters modeling the interactions of the metal ion of interest with water and protein ligands. Previously, we had developed a CTPOL PEF for protein simulations of Zn(2+) bound to Cys(-) and/or His(0) that includes charge transfer and local polarization effects as well as metal van der Waals parameters that reproduce the structural and thermodynamical properties of 22 dications. Here, we evaluate if the CTPOL PEF and the new metal parameters (referred to as the CTPOLa force field) can be applied to proteins containing polynuclear metal-binding sites and heavy toxic metal ions, using the CdZn(2)-Cys(9) beta-domain of rat liver metallothionein-2 and the Hg(2+)-bound 18-residue peptide from MerP as test systems. Using the CTPOLa force field, simulations of the beta-domain of rat liver metallothionein-2 totaling 19 ns could preserve the experimentally observed CdZn(2)-Cys(9) complex geometry and overall protein structure, whereas simulations neglecting charge transfer and local polarization effects could not. However, the CTPOLa force field cannot reproduce the experimentally observed linear bicoordination of Hg(2+) in the MerP peptide without adding an angular restraint to the CTPOL PEF to correct the angle distribution about Hg(2+). Thus, the force fields presented herein for the group IIB metal ions can be applied to simulation studies of proteins containing polynuclear metal-binding sites and heavy metal ions in aqueous solution. PEF neglecting charge transfer and local polarization effects in conjunction with vdW parameters adjusted to reproduce the structural and thermodynamical properties of only the metal ion in question could not yield an accurate representation of the metal-binding site and overall protein structure.

Self-consistent polarization neglect of diatomic differential overlap: application to water clusters

Semiempirical self-consistent field (SCF) methods based on the neglect of diatomic differential overlap (NDDO) formalism have the ability to treat the formation and breaking of chemical bonds but have been found to poorly describe hydrogen bonding and weak electrostatic complexes. In contrast, most empirical potentials are not able to describe bond breaking and formation but have the ability to add missing elements of hydrogen bonding by using classical electrostatic interactions. We present a new method which combines aspects of both NDDO-based SCF techniques and classical descriptions of polarization to describe the diffuse nature of the electronic wavefunction in a self-consistent manner. We develop the "self-consistent polarization neglect of diatomic differential overlap" (SCP-NDDO) theory with the additional description of molecular dispersion developed as a second-order perturbation theory expression. The current study seeks to model water-water interactions as a test case. To this end, we have parametrized the method to accurate ab initio complete basis set limit estimates of small water cluster binding energies of Xantheas and co-workers [J. Chem. Phys. 116, 1493 (2002); 120, 823 (2004)]. Overall agreement with the ab initio binding energies (n=2-6, and 8) is achieved with a rms error of 0.19 kcal/mol. We achieve noticeable improvements in the structure, vibrational frequencies, and energetic predictions of water clusters (n< or =21) relative to standard NDDO-based methods.

Structural prediction of the beta-domain of metallothionein-3 by molecular dynamics simulation

The beta-domain of metallothionein-3 (MT3) has been reported to be crucial to the neuron growth inhibitory bioactivity. Little detailed three-dimensional structural information is available to present a reliable basis for elucidation on structure-property-function relationships of this unique protein by experimental techniques. So, molecular dynamics simulation is adopted to study the structure of beta-domain of MT3. In this article, a 3D structural model of beta-domain of MT3 was generated. The molecular simulations provide detailed protein structural information of MT3. As compared with MT2, we found a characteristic conformation formed in the fragment (residue 1-13) at the N-terminus of MT3 owing to the constraint induced by 5TCPCP9, in which Pro7 and Pro9 residues are on the same side of the protein, both facing outward and the two 5-member rings of prolines are arranged almost in parallel, while Thr5 is on the opposite side. Thr5 in MT3 is also found to make the first four residues relatively far from the fragment (residue 23-26) as compared with MT2. The simulated structure of beta-domain of MT3 is looser than that of MT2. The higher energy of MT3 than that of MT2 calculated supports these conclusions. Simulation on the four isomer arising from the cis- or trans-configuration of 6CPCP9 show that the trans-/trans-isomer is energetic favorable. The partially unfolding structure of beta-domain of MT3 is also simulated and the results show the influence of 6CPCP9 sequence on the correct folding of this domain. The correlations between the bioactivity of MT3 and the simulated structure as well as the folding of beta-domain of MT3 are discussed based on our simulation and previous results.

Characterization of the conformational changes in recombinant human metallothioneins using ESI-MS and molecular modeling

Electrospray ionization mass spectrometry (ESI-MS) data and molecular modeling calculations were used to gain mechanistic, conformational, and domain-specific information from the acid-induced demetallation reactions of human metallothionein. The recombinant proteins studied were the single α- and β-rhMT-1a domains and the βα- and αβ-rhMT-1a two-domain species, based on the human metallothionein 1a sequence. Complete molecular models (MM3/MD) for all the fully metallated and demetallated species using a modified force field are reported for the first time. Basic residues that contribute to the ESI-MS charge states are identified from the molecular models. Demetallation took place under equilibrium conditions within a narrow pH range. For the two-domain proteins, these results support a demetallation mechanism involving the initial complete demetallation of one domain followed by the other for both βα-rhMT and αβ-rhMT. Based on the stability of the separate domains, the β domain is predicted to demetallate first in the two-domain rhMTs. Both the α domain and the β domain were observed to bind an excess of one Cd2+ ion. The metallated rhMT structures were shown to have very stable conformations, but only when fully metallated. Two or more conformations were observed at low pH in the ESI-MS data, which are interpreted as arising from the presence of structure, as opposed to a random coil, in the apo-rhMT. This is the first report of the existence of a structure in the two-domain metal-free apo-MT proteins. Only at extremely low pH does the structure open fully to give the highest charge distribution, which is associated with a random coil. Pre-existing structural features in the apo-MT would explain why the metallation reactions occur so rapidly.Key words: recombinant human metallothionein-1 (rhMT1), electrospray ionization mass spectrometry (ESI-MS), circular dichroism (CD), molecular mechanics/molecular dynamics (MM3/MD).

Peptide folding, metal-binding mechanisms, and binding site structures in metallothioneins

This minireview specifically focuses on recent studies carried out on structural aspects of metal-free metallothionein (MT), the mechanism of metal binding for copper and arsenic, structural studies using x-ray absorption spectroscopy and molecular mechanics modeling, and speciation studies of a novel cadmium and arsenic binding algal MT. Molecular mechanics-molecular dynamics calculations of apo-MT show that significant secondary structural features are retained by the polypeptide backbone upon sequential removal of the metal ions, which is stabilized by a possible H-bonding network. In addition, the cysteinyl sulfurs were shown to rotate from within the domain core, where they are found in the metallated state, to the exterior surface of the domain, suggesting an explanation for the rapid metallation reactions that were measured. Mixing Cu6beta-MT with Cd4alpha-MT and Cu6alpha-MT with Cd3beta-MT resulted in redistribution of the metal ions to mixed metal species in each domain; however, the Cu+ ions preferentially coordinated to the beta domain in each case. Reaction of As3+ with the individual metal-free beta and alpha domains of MT resulted in three As3+ ions coordinating to each of the domains, respectively, in a proposed distorted trigonal pyramid structure. Kinetic analysis provides parameters that allow simulation of the binding of each of the As3+ ions. X-ray absorption spectroscopy provides detailed information about the coordination environment of the absorbing element. We have combined measurement of x-ray absorption near edge structure (XANES) and extended x-ray absorption fine structure (EXAFS) data with extensive molecular dynamics calculations to determine accurate metal-thiolate structures. Simulation of the XANES data provides a powerful technique for probing the coordination structures of metals in metalloproteins. The metal binding properties of an algal MT, Fucus vesiculosus, has been investigated by UV absorption and circular dichroism spectroscopy and electrospray ionization-mass spectrometry. The 16 cysteine residues of this algal MT were found to coordinate six Cd2+ ions in two domains with stoichiometries of a novel Cd3S7 cluster and a beta-like Cd3S9 cluster.

The GROMOS software for biomolecular simulation: GROMOS05

We present the latest version of the Groningen Molecular Simulation program package, GROMOS05. It has been developed for the dynamical modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization. An overview of GROMOS05 is given, highlighting features not present in the last major release, GROMOS96. The organization of the program package is outlined and the included analysis package GROMOS++ is described. Finally, some applications illustrating the various available functionalities are presented.

Molecular dynamics study on the folding and metallation of the individual domains of metallothionein

De novo synthesis of metallothionein (MT) initially forms the metal-free protein, which must, in a posttranslational reaction, coordinate metal ions via the cysteine sulfur ligands to form the fully folded protein structure. In this article, we use molecular dynamics (MD) and molecular mechanics (MM) to investigate the metal-dependent folding steps of the individual domains of recombinant human metallothionein (MT). The divalent metals were removed sequentially from the metal-sulfur M4(Scys)11 and M3(Scys)9 clusters within the alpha- and beta- domains of MT, respectively, after protonation of the previously coordinating sulfurs. With each of the four (alpha) or three (beta) sites defined, an order of metal release could be determined on the basis of a comparison of the strain energies for each combination by selecting the lowest energy demetallated conformations. The effect of an additional noninteracting, 34-residue peptide sequence on the demetallation order was assessed when bound to either the N- or C-termini of the individual domain fragments to identify the differences in cluster stability between one- and two-domain proteins. The N-terminal-bound peptide had no effect on the order of metal removal; however, addition to the C-terminus significantly altered the sequence. The number of hydrogen bonds was calculated for each energy-minimized demetallated structure and was increased on metal removal, indicating a possible stabilization mechanism for the protein structure via a hydrogen-bonding network. On complete demetallation, the cysteinyl sulfurs were shown to move to the exterior surface of the peptide chain.

Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A

Botulinum neurotoxin serotype A (BoNTA) is one of the most toxic substances known. Currently, there is no antidote to BoNTA. Small molecules identified from high-throughput screening reportedly inhibit the endopeptidase--the zinc-bound, catalytic domain of BoNTA--at a drug concentration of 20 microM. However, optimization of these inhibitors is hampered by challenges including the computational evaluation of the ability of a zinc ligand to compete for coordination with nearby residues in the active site of BoNTA. No improved inhibitor of the endopeptidase has been reported. This article reports the development of a serotype-selective, small-molecule inhibitor of BoNTA with a K(i) of 12 microM. This inhibitor was designed to coordinate the zinc ion embedded in the active site of the enzyme for affinity and to interact with a species-specific residue in the active site for selectivity. It is the most potent small-molecule inhibitor of BoNTA reported to date. The results suggest that multiple molecular dynamics simulations using the cationic dummy atom approach are useful to structure-based design of zinc protease inhibitors.

XAFS Spectral Analysis of the Cadmium Coordination Geometry in Cadmium Thiolate Clusters in Metallothionein

We report the combination of measurement and prediction of X-ray absorption fine structure (XAFS) data, where the term XAFS refers to the overall spectrum that encompasses both the X-ray Absorption Near Edge Structure (XANES) region as well as the Extended X-ray Absorption Fine Structure (EXAFS) region, to evaluate the cadmium thiolate cluster structures in the metalloprotein metallothionein. XAFS spectra were simulated using coordinates from molecular models of the protein calculated by molecular mechanics/molecular dynamics (MM3/MD), from NMR analyses, and from analysis of X-ray diffraction data. XAFS spectra were also simulated using the coordinates from X-ray crystallographic data for [Cd(SPh)4]2-, CdS, [Cd2(mu-SPh)2(SPh)4]2-, and [Cd4(mu-SPh)6(SPh)4]2-. The simulated XAFS data that were calculated using the FEFF8 program closely resemble the experimental data reported for [Cd(SPh)4]2-, CdS, [Cd2(mu-SPh)2(SPh)4]2-, [Cd4(mu-SPh)6(SPh)4]2-, rabbit liver metallothionein cadmium alpha-domain (Cd4-alpha MT), and cadmium rabbit liver betaalpha metallothionein (Cd7-betaalpha MT). MM3 force field parameters were modified to include cadmium-sulfur bonding and were initially set to values derived from published X-ray diffraction and EXAFS experimental data. The force field was further calibrated and adjusted through comparison between experimental spectra taken from the literature and simulated XAFS spectra calculated using the FEFF8 program in combination with atomic coordinates from MM3/MD energy minimization. MM3/MD techniques were used with the calibrated force field to predict the high-resolution structure of the metal clusters in rabbit liver Cd7-MT. Structures for Cd3S9 (beta) MT and Cd4S11 (alpha) MT domains from MM3/MD calculations and those previously reported for Cd7-MT on the basis of 1H and 113Cd NMR data were compared. Structural differences between the different models for these cadmium thiolate clusters were evident. Combining the measurement and simulation of XAFS data provides an excellent method of assessing, modeling, and predicting metal-binding sites in metalloproteins when X-ray absorption spectroscopy (XAS) data are available.

KvAP-based model of the pore region of shaker potassium channel is consistent with cadmium- and ligand-binding experiments

Potassium channels play fundamental roles in excitable cells. X-ray structures of bacterial potassium channels show that the pore-lining inner helices obstruct the cytoplasmic entrance to the closed channel KcsA, but diverge in widely open channels MthK and KvAP, suggesting a gating-hinge role for a conserved Gly in the inner helix. A different location of the gating hinge and a narrower open pore were proposed for voltage-gated Shaker potassium channels that have the Pro-473-Val-Pro motif. Two major observations back the proposal: cadmium ions lock mutant Val-476-Cys in the open state by bridging Cys-476 and His-486 in adjacent helices, and cadmium blocks the locked-open double mutant Val-474-Cys/Val-476-Cys by binding to Cys-474 residues. Here we used molecular modeling to show that the open Shaker should be as wide as KvAP to accommodate an open-channel blocker, correolide. We further built KvAP-, MthK-, and KcsA-based models of the Shaker mutants and Monte-Carlo-minimized them with constraints Cys-476-Cd(2+)-His-486. The latter were consistent with the KvAP-based model, causing a small-bend N-terminal to the Pro-473-Val-Pro motif. The constraints significantly distorted the MthK-based structure, making it similar to KvAP. The KcsA structure resisted the constraints. Two Cd(2+) ions easily block the locked-open KvAP-based model at Cys-474 residues, whereas constraining a single cadmium ion to four Cys-474 caused large conformational changes and electrostatic imbalance. Although mutual disposition of the voltage-sensor and pore domains in the KvAP x-ray structure is currently disputed, our results suggest that the pore-region domain retains a nativelike conformation in the crystal.

Amsacta moorei entomopoxvirus expresses an active superoxide dismutase

The entomopoxvirus from Amsacta moorei serves as the prototype of the group B entomopoxviruses. One of the interesting genes found in Amsacta moorei entomopoxvirus (AmEPV) is a superoxide dismutase (sod) (open reading frame AMV255). Superoxide dismutases (SODs) catalyze the conversion of superoxide radicals to hydrogen peroxide and oxygen. Many vertebrate poxviruses contain a sod gene, but to date, none have been demonstrated to be active. There are three families of SODs, characterized by their metal ion-binding partners, Fe, Mn, or Cu and Zn. Poxvirus enzymes belong to the Cu-Zn SOD family. Unlike inactive vertebrate poxvirus SODs, AMVSOD contains all the amino acids necessary for function. We expressed and purified a 6X-His-tagged version of the AMVSOD in Escherichia coli. The recombinant AMVSOD demonstrates superoxide dismutase activity both in an in situ gel assay and by stopped flow spectrophotometry. The k(cat)/K(m) for AMVSOD is 4 x 10(7) M(-1)s(-1). In infected cells, the AMVSOD protein behaves as a dimer and is catalytically active; however, disruption of the gene in AMEPV has little or no effect on growth of the virus in cell culture. An analysis of mRNA expression indicates that AMVsod is expressed late during infection of Lymantria dispar (Ld652) cells and produces a discrete nonpolydisperse transcript. Characterization of protein expression with a monoclonal antibody generated against AMVSOD confirms that the AMVSOD protein can be classified as a late, postreplicative gene. Therefore, AMVSOD is the first example of an active poxvirus SOD.

A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and biologically active systems

The implementation of a hybrid QM-MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree-Fock and density functional methods and varying QM-MM boundaries. Also, the computationally efficient RI-J method has been examined for use in QM-MM applications. A B(12) cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM-MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes.

Molecular dynamics simulations of metalloproteins

Molecular dynamics simulations are now commonly applied to metalloproteins, despite the challenges introduced by the presence of metal ions. Force field parameters are nowadays available also for these 'exotic' atoms and several biological systems have been successfully studied. Some of the most relevant results and methodological advancements are reviewed.

Combined quantum and molecular mechanics calculations on metalloproteins

The combination of quantum mechanics and molecular mechanics (QM/MM) methods is one of the most promising approaches to study the structure, function and properties of proteins. The number of QM/MM applications on metalloproteins is steadily increasing, especially studies with density functional methods on redox-active metal centres. Recent developments include new parameterised methods to treat covalent bonds between the quantum and classical systems, methods to obtain free energy from QM/MM results, and the combination of quantum chemistry and protein crystallography.

Advances in the structure and chemistry of metallothioneins

A low molecular weight (6-7 kDa) class of metalloproteins, designated as metallothioneins (MTs), exhibit repeated sequence motifs of either CxC or CxxC through which mono or divalent d(10) metal ions are bound in polymetallic-thiolate clusters. The preservation of metal-thiolate clusters in an increasing number of three-dimensional structures of these proteins signifies the importance of this structural motif. This review focuses on the recent developments regarding the versatile and striking chemical reactivity of MTs as well as on the existence of conformational/configurational dynamics within their structure. Both properties and their interplay are likely to be essential for the still elusive biological function of these proteins.

Simulating enzyme reactions: challenges and perspectives

Elucidating how enzymes enhance the rates of the reactions that they catalyze is a major goal of contemporary biochemistry, and it is an area in which computational and theoretical techniques can make a major contribution. This article outlines some of the processes that need to be investigated if enzyme catalysis is to be understood, reviews the current state-of-the-art in enzyme simulation work, and highlights challenges for the future.

Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method

I report herein two 2.0 ns (1.0 fs time step) MD simulations of two zinc complexes bridged by a hydroxide in phosphotriesterase (PTE) employing the nonbonded method and the cationic dummy atom method that uses virtual atoms to impose orientational requirement for zinc ligands. The cationic dummy atom method was able to simulate the four-ligand coordination of the two zinc complexes in PTE. The distance (3.39 +/- 0.07A) between two nearby zinc ions in the time-average structure of PTE derived from the MD simulation using the cationic dummy atoms matched that in the X-ray structure (3.31 +/- 0.001A). Unequivocally, the time-average structure of PTE was able to fit into the experimentally determined difference electron density map of the corresponding X-ray structure. The results demonstrate the practicality of the cationic dummy atom method for MD simulations of zinc proteins bound with multiple zinc ions. In contrast, a 2.0 ns (1.0 fs time step) MD simulation using the nonbonded method revealed a striking difference in the active site between the X-ray structure and the time-average structure that was unable to fit into the density map of PTE. The results suggest that caution should be used in the MD simulations using the nonbonded method.

New developments in applying quantum mechanics to proteins

Algorithmic improvements of quantum mechanical methodologies have increased our ability to study the electronic structure of fragments of a biomolecule (e.g. an enzyme active site) or entire biomolecules. Three main strategies have emerged as ways in which quantum mechanics can be applied to biomolecules. The supermolecule approach continues to be utilized, but it is slowly being replaced by the so-called coupled quantum mechanical/molecular mechanical methodologies. An exciting new direction is the continued development and application of linear-scaling quantum mechanical approaches to biomolecular systems.