Molecular mechanics models for tetracycline analogs

Tetracyclines (Tcs) are an important family of antibiotics that bind to the ribosome and several proteins. To model Tc interactions with protein and RNA, we have developed a molecular mechanics force field for 12 tetracyclines, consistent with the CHARMM force field. We considered each Tc variant in its zwitterionic tautomer, with and without a bound Mg(2+). We used structures from the Cambridge Crystallographic Data Base to identify the conformations likely to be present in solution and in biomolecular complexes. A conformational search by simulated annealing was undertaken, using the MM3 force field, for tetracycline, anhydrotetracycline, doxycycline, and tigecycline. Resulting, low-energy structures were optimized with an ab initio method. We found that Tc and its analogs all adopt an extended conformation in the zwitterionic tautomer and a twisted one in the neutral tautomer, and the zwitterionic-extended state is the most stable in solution. Intermolecular force field parameters were derived from a standard supermolecule approach: we considered the ab initio energies and geometries of a water molecule interacting with each Tc analog at several different positions. The final, rms deviation between the ab initio and force field energies, averaged over all forms, was 0.35 kcal/mol. Intramolecular parameters were adopted from either the standard CHARMM force field, the ab initio structure, or the earlier, plain Tc force field. The model reproduces the ab initio geometry and flexibility of each Tc. As tests, we describe MD and free energy simulations of a solvated complex between three Tcs and the Tet repressor protein.     

Ab initio folding of helix bundle proteins using molecular dynamics simulations

We have demonstrated that ab initio fast folding simulations at 400 K using a GB implicit solvent model with an all-atom based force field can describe the spontaneous formation of nativelike structures for the 36-residue villin headpiece and the 46-residue fragment B of Staphylococcal protein A. An implicit solvent model combined with high-temperature MD makes it possible to perform direct folding simulations of small- to medium-sized proteins by reducing the computational requirements tremendously. In the early stage of folding of the villin headpiece and protein A, initial hydrophobic collapse and rapid formation of helices were found to play important roles. For protein A, the third helix forms first in the early stage of folding and exhibits higher stability. The free energy profiles calculated from the folding simulations suggested that both of the helix-bundle proteins show a two-state thermodynamic behavior and protein A exhibits rather broad native basins.     

First principles and classical molecular dynamics simulations of solvated benzene

We have performed extensive ab initio and classical molecular dynamics (MD) simulations of benzene in water in order to examine the unique solvation structures that are formed. Qualitative differences between classical and ab initio MD simulations are found and the importance of various technical simulation parameters is examined. Our comparison indicates that nonpolarizable classical models are not capable of describing the solute-water interface correctly if local interactions become energetically comparable to water hydrogen bonds. In addition, a comparison is made between a rigid water model and fully flexible water within ab initio MD simulations which shows that both models agree qualitatively for this challenging system.     

On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations

During the past years, the use of combined quantum-classical, QM/MM, methods for the study of complex biomolecular processes, such as enzymatic reactions and photocycles, has increased considerably. The quality of the results obtained from QM/MM calculations is largely dependent on five aspects to be considered when setting up a molecular model: the QM Hamiltonian, the MM Hamiltonian or force field, the boundary and coupling between the QM and MM regions, the size of the QM region and the boundary condition for the MM region. In this study, we systematically investigate the influence of a variation of the molecular mechanics force field and the size of the QM region in QM/MM MD simulations on properties of the photoactive part of the blue light photoreceptor protein AppA. For comparison, we additionally performed classical MD simulations and studied the effect of a variation of the type of spatial boundary condition. The classical boundary conditions and the force field used in a QM/MM MD simulation are shown to have non-neglegible effects upon the structural and energetic properties of the protein which makes it advisable to minimize computational artifacts in QM/MM MD simulations by application of periodic boundary conditions and a thermodynamically calibrated force field. A comparison of the structural and energetic properties of MD simulations starting from two alternative, different X-ray structures for the blue light utilizing flavin protein in its dark state indicates a slight preference of the two force fields used for the so-called Anderson structure over the Jung structure.     

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation

The accurate characterization of the structure and dynamics of proteins in disordered states is a difficult problem at the frontier of structural biology whose solution promises to further our understanding of protein folding and intrinsically disordered proteins. Molecular dynamics (MD) simulations have added considerably to our understanding of folded proteins, but the accuracy with which the force fields used in such simulations can describe disordered proteins is unclear. In this work, using a modern force field, we performed a 200 μs unrestrained MD simulation of the acid-unfolded state of an experimentally well-characterized protein, ACBP, to explore the extent to which state-of-the-art simulation can describe the structural and dynamical features of a disordered protein. By comparing the simulation results with the results of NMR experiments, we demonstrate that the simulation successfully captures important aspects of both the local and global structure. Our simulation was ~2 orders of magnitude longer than those in previous studies of unfolded proteins, a length sufficient to observe repeated formation and breaking of helical structure, which we found to occur on a multimicrosecond time scale. We observed one structural feature that formed but did not break during the simulation, highlighting the difficulty in sampling disordered states. Overall, however, our simulation results are in reasonable agreement with the experimental data, demonstrating that MD simulations can already be useful in describing disordered proteins. Finally, our direct calculation of certain NMR observables from the simulation provides new insight into the general relationship between structural features of disordered proteins and experimental NMR relaxation properties.     

Urea: an ab initio and force field study of the gas and solid phases

We have studied the gaseous and solid phases of urea using both quantum mechanics calculation and force field simulation methods. Our ab initio calculations confirmed experimental observations that urea structure is planar in the crystal, but nonplanar in the gas phase. Based on electron structure analysis, we suggest that the significant difference between these two structures in different environments can be qualitatively explained by two resonance structures. The planar structure is more polarized than the nonplanar one, and the former is stabilized in the solid phases due to strong electrostatic interactions. We found classical force field method is incapable to represent such strong polarization effect. Using molecular dynamics simulations with a force field optimized for condensed phases, we calculated the crystalline structures of urea in the temperature range of 12 to 293 K. The densities as well as cell parameters are within 2% deviation from the experimental data in the temperature range.     

Development of a force field for Li(2)SiF(6)

A force field has been developed for Li(2)SiF(6) for subsequent use in Molecular Dynamics (MD) simulations involving Li(+) and SiF(2-) (6) ions in a polymer electrolyte host. Both ab initio calculations and available empirical data have been used. The force field has been verified in simulations of the crystal structure of Li(2)SiF(6) in two different space groups: P321 and P3(-)m1. The use of MD simulation to assess the correct space group for Li(2)SiF(6) shows that it is probably P321.     

Development and validation of empirical force field parameters for netropsin

The netropsin molecule preferentially binds to the four consecutive A.T base pairs of the DNA minor groove and could therefore inhibit the expression of specific genes. The understanding of its binding on a molecular level is indispensable for computer-aided design of new antitumor agents. This knowledge could be obtained via molecular dynamics (MD) and docking simulations, but in this case appropriate force field parameters for the netropsin molecule should be explicitly defined. Our parametrization was based on the results of quantum chemical calculations. The resulting set of parameters was able to reproduce bond lengths, bond angles, torsional angles of the ab initio minimized geometry within 0.03 A, 3 deg and 5 deg, respectively, and its vibrational frequencies with a relative error of 4.3% for low and 2.8% for high energy modes. To show the accuracy of the developed parameters we calculated an IR spectrum of the netropsin molecule using MD simulation and found it to be in good agreement with the experimental one. Finally, we performed a 10 ns long MD simulation of the netropsin-DNA complex immersed in explicit water. The overall complex conformation remained stable at all times, and its secondary structure was well retained.     

Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics

We have run several molecular dynamics (MD) simulations on zinc-containing phosphotriesterase (PTE) with two bound substrates, sarin and paraoxon, and with the substrate analog diethyl 4-methylbenzylphosphonate. A standard nonbonded model was employed to treat the zinc ions with the commonly used charge of +2. In all the trajectories, we observed a tightly bound water (TBW) molecule in the active site that was coordinated to the less buried zinc ion. The phosphoryl oxygen of the substrate/inhibitor was found to be coordinated to the same zinc ion so that, considering all ligands, the less buried zinc was hexa-coordinated. The hexa-coordination of this zinc ion was not seen in the deposited X-ray pdb files for PTE. Several additional MD simulations were then performed using different charges (+1, +1.5) on the zinc ions, along with ab initio and density functional theory (DFT) calculations, to evaluate the following possibilities: the crystal diffraction data were not correctly interpreted; the hexa-coordinated zinc ion in PTE is only present in solution and not in the crystal; and the hexa-coordinated zinc ion in PTE is an artifact of the force field used. A charge of +1.5 leads to a coordination number (CN) of 5 on both zinc ions, which is consistent with the results from ab initio and DFT calculations and with the latest high resolution X-ray crystal structure. The commonly used charge of +2 produces a CN of 6 on the less buried zinc. The CN on the more buried zinc ion is 5 when the substrate/inhibitor is present in the simulation, and increases to 6 when the substrate/inhibitor is removed prior to the simulation. The results of both of the MD and quantum mechanical calculations lead to the conclusion that the zinc ions in the PTE active site are both penta-coordinated, and that the MD simulations performed with the charge of +2 overestimate the CN of the zinc ions in the PTE active site. The overall protein structures in the simulations remain unaffected by the change in zinc charge from +2 to +1.5. The results also suggest that the charge +1.5 is the most appropriate for the molecular dynamics simulations on zinc-containing PTE when a nonbonded model is used and no global thermodynamic conclusion is sought. We also show that the standard nonbonded model is not able to properly treat the CN and energy at the same time. A preliminary, promising charge-transfer model is discussed with the use of the zinc charge of +1.5.     

Prediction of protein–protein complexes using replica exchange with repulsive scaling

The realistic prediction of protein–protein complex structures is import to ultimately model the interaction of all proteins in a cell and for the design of new protein–protein interactions. In principle, molecular dynamics (MD) simulations allow one to follow the association process under realistic conditions including full partner flexibility and surrounding solvent. However, due to the many local binding energy minima at the surface of protein partners, MD simulations are frequently trapped for long times in transient association states. We have designed a replica-exchange based scheme employing different levels of a repulsive biasing between partners in each replica simulation. The bias acts only on intermolecular interactions based on an increase in effective pairwise van der Waals radii (repulsive scaling (RS)-REMD) without affecting interactions within each protein or with the solvent. For a set of five protein test cases (out of six) the RS-REMD technique allowed the sampling of near-native complex structures even when starting from the opposide site with respect to the native binding site for one partner. Using the same start structures and same computational demand regular MD simulations sampled near native complex structures only for one case. The method showed also improved results for the refinement of docked structures in the vicinity of the native binding geometry compared to regular MD refinement.     

Evaluation of the effect of the chiral centers of Taxol on binding to β-tubulin: A docking and molecular dynamics simulation study

Taxol is one of the most important anti-cancer drugs. The interaction between different variants of Taxol, by altering one of its chiral centers at a time, with β-tubulin protein has been investigated. To achieve such goal, docking and molecular dynamics (MD) simulation studies have been performed. In docking studies, the preferred conformers have been selected to further study by MD method based on the binding energies reported by the AutoDock program. The best result of docking study which shows the highest affinity between ligand and protein has been used as the starting point of the MD simulations. All of the complexes have shown acceptable stability during the simulation process, based on the RMSDs of the backbone of the protein structure. Finally, MM-GBSA calculations have been carried out to select the best ligand, considering the binding energy criteria. The results predict that two of the structures have better affinity toward the mentioned protein, in comparison with Taxol. Three of the structures have affinity similar to that of the Taxol toward the β-tubulin.     

A force field for monosaccharides and (1 → 4) linked polysaccharides

A force field for monosaccharides that can be extended to (1 → 4) linked polysaccharides has been developed for the AMBER potential function. The resulting force field is consistent with the existing AMBER force field for proteins and nucleic acids. Modifications to the standard AMBER OH force constant and to the Lennard-Jones parameters were made. Furthermore, a 10–12 nonbonded term was included between the hydroxyl hydrogen of the saccharide and the water oxygen (TIP3P, SPC/E, etc.) to reproduce better the water–saccharide intermolecular distances. STO-3G electrostatic potential (ESP) charges were used to represent the electrostatic interactions between the saccharide and its surrounding environment. To obtain charges for polysaccharides, a scheme was developed to piece together saccharide residues through 1 → 4 connections while still retaining a net neutral charge on the molecule as a whole. Free energy perturbation (FEP) simulations of D -glucose and D -mannose in water were performed to test the resulting force field. The FEP simulations demonstrate that AMBER overestimates intramolecular interaction energies, suggesting that further improvements are needed in this part of the force field. To test further the reliability of the parameters, a molecular dynamics (MD) simulation of α-D -glucose in water was also performed. The MD simulation was able to produce structural and conformational results that are in accord with experimental evidence and previous theoretical results. Finally, a relaxed conformational map of β-maltose was assembled and it was found that the present force field is consistent with available theoretical and experimental results. © 1994 by John Wiley & Sons, Inc.     

The tetracycline: Mg2+ complex: a molecular mechanics force field

Tetracycline (Tc) is an important antibiotic, which binds specifically to the ribosome and several proteins, in the form of a Tc-:Mg2+ complex. To model Tc:protein and Tc:RNA interactions, we have developed a molecular mechanics force field model of Tc, which is consistent with the CHARMM force field for proteins and nucleic acids. We used structures from the Cambridge Crystallographic Data Base to identify the main Tc conformations that are likely to be present in solution and in biomolecular complexes. A conformational search was also done, using the MM3 force field to perform simulated annealing of Tc. Several resulting, low-energy structures were optimized with an ab initio model and used in developing the new Tc force field. Atomic charges and Lennard-Jones parameters were derived from a supermolecule ab initio approach. We considered the ab initio energies and geometries of a probe water molecule interacting with Tc at 36 different positions. We considered both a neutral and a zwitterionic Tc form, with and without bound Mg2+. The final rms deviation between the ab initio and force field energies, averaged over all forms, was just 0.35 kcal/mol. The model also reproduces the ab initio geometry and flexibility of Tc. As further tests, we did simulations of a Tc crystal, of Tc:Mg2+ and Tc:Ca2+ complexes in aqueous solution, and of a solvated complex between Tc:Mg2+ and the Tet repressor protein (TetR). With slight, ad hoc adjustments, the model can reproduce the experimental, relative, Tc binding affinities of Mg2+ and Ca2+. It performs well for the structure and fluctuations of the Tc:Mg2+:TetR complex. The model should therefore be suitable to investigate the interactions of Tc with proteins and RNA. It provides a starting point to parameterize other compounds in the large Tc family.     

New-generation amber united-atom force field

We have developed a new-generation Amber united-atom force field for simulations involving highly demanding conformational sampling such as protein folding and protein-protein binding. In the new united-atom force field, all hydrogens on aliphatic carbons in all amino acids are united with carbons except those on Calpha. Our choice of explicit representation of all protein backbone atoms aims at minimizing perturbation to protein backbone conformational distributions and to simplify development of backbone torsion terms. Tests with dipeptides and solvated proteins show that our goal is achieved quite successfully. The new united-atom force field uses the same new RESP charging scheme based on B3LYP/cc-pVTZ//HF/6-31g** quantum mechanical calculations in the PCM continuum solvent as that in the Duan et al. force field. van der Waals parameters are empirically refitted starting from published values with respect to experimental solvation free energies of amino acid side-chain analogues. The suitability of mixing new point charges and van der Waals parameters with existing Amber covalent terms is tested on alanine dipeptide and is found to be reasonable. Parameters for all new torsion terms are refitted based on the new point charges and the van der Waals parameters. Molecular dynamics simulations of three small globular proteins in the explicit TIP3P solvent are performed to test the overall stability and accuracy of the new united-atom force field. Good agreements between the united-atom force field and the Duan et al. all-atom force field for both backbone and side-chain conformations are observed. In addition, the per-step efficiency of the new united-atom force field is demonstrated for simulations in the implicit generalized Born solvent. A speedup around two is observed over the Duan et al. all-atom force field for the three tested small proteins. Finally, the efficiency gain of the new united-atom force field in conformational sampling is further demonstrated with a well-known toy protein folding system, an 18 residue polyalanine in distance-dependent dielectric. The new united-atom force field is at least a factor of 200 more efficient than the Duan et al. all-atom force field for ab initio folding of the tested peptide.     

Effects of mussel-inspired co-deposition of 2-hydroxymethyl methacrylate and poly (2-methoxyethyl acrylate) on the hydrophilicity and binding tendency of common hemodialysis membranes: Molecular dynamics simulations and molecular docking studies

Despite advances in the field, hemoincompatibility remains a critical issue for hemodialysis (HD) as interactions between various human blood constituents and the polymeric structure of HD membranes results in complications such as activation of immune system cascades. Adding hydrophilic polymer structures to the membranes is one modification approach that can decrease the extent of protein adsorption. This study conducted molecular dynamics (MD) simulations to understand the interactions between three human serum proteins (fibrinogen [FB], human serum albumin, and transferrin) and common HD membranes in untreated and modified forms. Poly(aryl ether sulfone) (PAES) and cellulose triacetate were used as the common dialyzer polymers, and membrane modifications were performed with 2-hydroxymethyl methacrylate (HEMA) and poly (2-methoxyethyl acrylate) (PMEA), using polydopamine-assisted co-deposition. The MD simulations were used as the framework for binding energy simulations, and molecular docking simulations were also performed to conduct molecular-level investigations between the two modifying polymers (HEMA and PMEA) and FB. Each of the three proteins acted differently with the membranes due to their unique nature and surface chemistry. The simulations show PMEA binds less intensively to FB with a higher number of hydrogen bonds, which reflects PMEA's superior performance compared to HEMA. The simulations suggest PAES membranes could be used in modified forms for blood-contact applications as they reflect the lowest binding energy to blood proteins.     

Molecular Dynamics Simulations of a β-Hairpin Fragment of Protein G by Means of Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics (ABEEMσπ/MM)

There are some controversial opinions about the origin of folding β‐hairpin stability in aqueous solution. In this study, the structural and dynamic behavior of a 16‐residue β‐hairpin from B1 domain of protein G has been investigated at 280, 300, 350 and 450 K using molecular dynamics (MD) simulations by means of Atom‐Bond Electronegativity Equalization Method Fused into Molecular Mechanics i.e., ABEEMδπ/MM and the explicit ABEEM‐7P water solvent model. In addition, a 300 K simulation of one mutant having the aromatic residues substituted with alanines has been performed. The hydrophobic surface area, hydrophilic surface area and some structural properties have been used to measure the role of the hydrophobic interactions. It is found that the aromatic residues substituted with alanines have shown an evident destabilization of the structure and unfolding started after 1.5 ns. It is also found that the number of the main chain hydrogen bonds have different distributions through three different simulations. All above demonstrate that the hydrophobic interactions and the main chain hydrogen bonds play an important role in the stability of the folding structure of β‐hairpin in solution. Furthermore, through the structural analyses of the β‐hairpin structures from four temperature simulations and the comparison with other MD simulations of β‐hairpin peptides, the new ABEEMδπ force field can reproduce the structural data in good agreement with the experimental data.     

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations

We have compared molecular dynamics (MD) simulations of a β-hairpin forming peptide derived from the protein Nrf2 with 10 biomolecular force fields using trajectories of at least 1 μs. The total simulation time was 37.2 μs. Previous studies have shown that different force fields, water models, simulation methods, and parameters can affect simulation outcomes. The MD simulations were done in explicit solvent with a 16-mer Nrf2 β-hairpin forming peptide using Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amber ff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, GROMOS96 53a6, CHARMM27, and OPLS-AA/L force fields. The effects of charge-groups, terminal capping, and phosphorylation on the peptide folding were also examined. Despite using identical starting structures and simulation parameters, we observed clear differences among the various force fields and even between replicates using the same force field. Our simulations show that the uncapped peptide folds into a native-like β-hairpin structure at 310 K when Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amber ff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, or GROMOS96 53a6 were used. The CHARMM27 simulations were able to form native hairpins in some of the elevated temperature simulations, while the OPLS-AA/L simulations did not yield native hairpin structures at any temperatures tested. Simulations that used charge-groups or peptide capping groups were not largely different from their uncapped counterparts with single atom charge-groups. On the other hand, phosphorylation of the threonine residue located at the β-turn significantly affected the hairpin formation. To our knowledge, this is the first study comparing such a large set of force fields with respect to β-hairpin folding. Such a comprehensive comparison will offer useful guidance to others conducting similar types of simulations.     

Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite the extensive effort. In this work, the folding process of the B domain of protein A (BdpA) has been simulated by both conventional and replica exchange molecular dynamics using AMBER FF03 all-atom force field. Started from an extended chain, a total of 40 conventional (each to 1.0 micros) and two sets of replica exchange (each to 200.0 ns per replica) molecular dynamics simulations were performed with different generalized-Born solvation models and temperature control schemes. The improvements in both the force field and solvent model allowed successful simulations of the folding process to the native state as demonstrated by the 0.80 A C(alpha) root mean square deviation (RMSD) of the best folded structure. The most populated conformation was the native folded structure with a high population. This was a significant improvement over the 2.8 A C(alpha) RMSD of the best nativelike structures from previous ab initio folding studies on BdpA. To the best of our knowledge, our results demonstrate, for the first time, that ab initio simulations can reach the native state of BdpA. Consistent with experimental observations, including Phi-value analyses, formation of helix II/III hairpin was a crucial step that provides a template upon which helix I could form and the folding process could complete. Early formation of helix III was observed which is consistent with the experimental results of higher residual helical content of isolated helix III among the three helices. The calculated temperature-dependent profile and the melting temperature were in close agreement with the experimental results. The simulations further revealed that phenylalanine 31 may play critical to achieve the correct packing of the three helices which is consistent with the experimental observation. In addition to the mechanistic studies, an ab initio structure prediction was also conducted based on both the physical energy and a statistical potential. Based on the lowest physical energy, the predicted structure was 2.0 A C(alpha) RMSD away from the experimentally determined structure.