Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy coinciding with the native binding site. The representative structure of the most stable cluster reproduced the experimental binding configuration, but an interesting conformational change in Hsp90 could be observed. The combined effects of solvation and ligand binding shift the equilibrium from a preferred loop-in conformation in the unbound state to an α-helical one in the bound state for the flexible lid region of Hsp90. Thus, our dynamic docking method is effective at predicting the native binding site while exhaustively sampling a wide configurational space, modulating the protein structure upon binding.     

Simple and accurate scheme to compute electrostatic interaction: Zero-dipole summation technique for molecular system and application to bulk water

The zero-dipole summation method was extended to general molecular systems, and then applied to molecular dynamics simulations of an isotropic water system. In our previous paper [I. Fukuda, Y. Yonezawa, and H. Nakamura, J. Chem. Phys. 134, 164107 (2011)], for evaluating the electrostatic energy of a classical particle system, we proposed the zero-dipole summation method, which conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple cutoff truncation. Here, we consider the application of this scheme to molecular systems, as well as some fundamental aspects of general cutoff truncation protocols. Introducing an idea to harmonize the bonding interactions and the electrostatic interactions in the scheme, we develop a specific algorithm. As in the previous study, the resulting energy formula is represented by a simple pairwise function sum, enabling facile applications to high-performance computation. The accuracy of the electrostatic energies calculated by the zero-dipole summation method with the atom-based cutoff was numerically investigated, by comparison with those generated by the Ewald method. We obtained an electrostatic energy error of less than 0.01% at a cutoff length longer than 13 A for a TIP3P isotropic water system, and the errors were quite small, as compared to those obtained by conventional truncation methods. The static property and the stability in an MD simulation were also satisfactory. In addition, the dielectric constants and the distance-dependent Kirkwood factors were measured, and their coincidences with those calculated by the particle mesh Ewald method were confirmed, although such coincidences are not easily attained by truncation methods. We found that the zero damping-factor gave the best results in a practical cutoff distance region. In fact, in contrast to the zero-charge scheme, the damping effect was insensitive in the zero-charge and zero-dipole scheme, in the molecular system we treated. We discussed the origin of this difference between the two schemes and the dependence of this fact on the physical system. The use of the zero damping-factor will enhance the efficiency of practical computations, since the complementary error function is not employed. In addition, utilizing the zero damping-factor provides freedom from the parameter choice, which is not trivial in the zero-charge scheme, and eliminates the error function term, which corresponds to the time-consuming Fourier part under the periodic boundary conditions.     

Formation of H3O+ from alcohols and ethers induced by intense laser fields

The processes of H₃O⁺ production from alcohols (ethanol, 2‐propanol, 1‐propanol, 2‐butanol) and ethers (diethyl ether and ethyl methyl ether), and their deuterium‐substituted species, by intense laser fields (800 nm, 100 fs, ～1 × 10¹⁴ W/cm) were investigated through time‐of‐flight (TOF) mass spectrometry. H₃O⁺ formation was observed for all these compounds except for ethyl methyl ether. From the analysis of TOF signals of H_(3?n)D_nO⁺ (n = 0, 1, 2, and 3) that have expanding tails with increasing flight time, it has been confirmed that the reaction proceeds through metastable dissociation from the intermediate species C₂H_(5?m)D_mO⁺(m = 0–5). The common shape of the H_(3?n)D_nO⁺ signal profiles contains two major distributions in the time constant, i.e., fast and slow components of <50 ns and ～500 ns, respectively. The H_(3?n)D_nO⁺ branching ratio is interpreted to be the result of complete scrambling of four hydrogen atoms at the C? C site in C₂H₄‐OH⁺, and partial exchange (18–38%) of a hydrogen atom in the OH group with four other hydrogen atoms within 1 ns prior to H_(3?n)D_nO⁺ production. Ab initio calculations for the isomers and transition states of C₂H₅O⁺ were also performed, and the observed H_(3?n)D_nO⁺ production mechanism has been discussed. In addition, a stable isomer having a complex structure and two isomerization pathways were discovered to contribute to the H₃O⁺ formation process. Copyright © 2010 John Wiley & Sons, Ltd.     

Folding of the 25 residue Abeta(12-36) peptide in TFE/water: temperature-dependent transition from a funneled free-energy landscape to a rugged one

The free-energy landscape of the Alzheimer beta-amyloid peptide Abeta(12-36) in a 40% (v/v) 2,2,2-trifluoroethanol (TFE)/water solution was determined by using multicanonical molecular dynamics simulations. Simulations using this enhanced conformational sampling technique were initiated from a random unfolded polypeptide conformation. Our simulations reliably folded the peptide to the experimental NMR structure, which consists of two linked helices. The shape of the free energy landscape for folding was found to be strongly dependent on temperature: Above 325 K, the overall shape was funnel-like, with the bottom of the funnel coinciding exactly with the NMR structure. Below 325 K, on the other hand, the landscape became increasingly rugged, with the emergence of new conformational clusters connected by low free-energy pathways. Finally, our simulations reveal that water and TFE solvate the polypeptide in different ways: The hydrogen bond formation between TFE and Abeta was enhanced with decreasing temperature, while that between water and Abeta was depressed.     

Computational analysis of ligand recognition mechanisms by prostaglandin E2 (subtype 2) and D2 receptors

The eight members of the prostanoid receptor family belong to the class A G protein-coupled receptors. We investigated the evolutionary relationship of the eight members by a molecular phylogenetic analysis and found that prostaglandin E₂ receptor subtype 2 (EP₂) and prostaglandin D₂ receptor (DP) were closely related. The structures of the ligands for the two receptors are similar to each other but are distinguished by the exchanged locations of the carbonyl oxygen and the hydroxy group in the cyclopentane ring. The ligand recognition mechanisms of the receptors were examined by an integrated approach using several computational methods, such as amino acid sequence comparison, homology modeling, docking simulation, and molecular dynamics simulation. The results revealed the similar location of the ligand between the two receptors. The common carboxy group of the ligands interacts with the Arg residue on the seventh transmembrane (TM) helix, which is invariant among the prostanoid receptors. EP₂ uses a Ser on TM1 to recognize the carbonyl oxygen in the cyclopentane ring of the ligand. The Ser is specifically conserved within EP₂. On the other hand, DP uses a Lys on TM2 to recognize the hydroxy group of the ?? chain of the ligand. The Lys is also specifically conserved within DP. The interaction network between the D(E)RY motif and TM6 was found in EP₂. However, DP lacked this network, due to the mutation in the D(E)RY motif. Based on these observations and the previously published mutational studies on the motif, the possibility of another activation mechanism that does not involve the interaction between the D(E)RY motif and TM6 will be discussed.     

Repeated‐annealing sampling combined with multicanonical algorithm for conformational sampling of bio‐molecules

A novel conformational sampling method (repeated‐annealing sampling method) is proposed to execute an efficient conformational sampling at a reasonable computational cost. In the method, a molecular dynamics simulation is done with repeating an elemental process. An elemental process consists of four subprocesses: high‐temperature run, annealing, room‐temperature run, and fast heating. The sampling is done automatically according to a temperature‐control schedule. The room‐temperature run is treated with the multicanonical algorithm, and the other subprocesses are done with the conventional molecular dynamics algorithm. The method, differing from the generalized ensemble methods recently developed, is not warrantable to give the canonical ensemble because of the nonphysical process in the annealing. However, we observed that the slower the annealing and the longer the high‐temperature run, the closer the sampled conformations to those of the canonical ensemble. A test was performed with tri‐N‐acetyl‐D ‐glucosamine in vacuo, and the results were compared with those from the conventional multicanonical simulation. Not only the reweighted canonical distribution function but also the energy landscape were in good agreement with those from the conventional multicanonical simulation. The potential of mean force also showed a fairly good agreement with that from the conventional multicanonical simulation in the room‐temperature region. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1098–1106, 2001     

Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems

We describe the application of a special purpose board for molecular dynamics simulations, named MDGRAPE-3, to the problem of simulating periodic bio-molecular systems. MDGRAPE-3 is the latest board in a series of hardware accelerators designed to calculate the nonbonding long-range interactions much more rapidly than normal processors. So far, MDGRAPEs were mainly applied to isolated systems, where very many nonbonded interactions were calculated without any distance cutoff. However, in order to regulate the density and pressure during simulations of membrane embedded protein systems, one has to evaluate interactions under periodic boundary conditions. For this purpose, we implemented the Particle-Mesh Ewald (PME) method, and its approximation with distance cutoffs and charge neutrality as proposed by Wolf et al., using MDGRAPE-3. When the two methods were applied to simulations of two periodic biomolecular systems, a single MDGRAPE-3 achieved 30-40 times faster computation times than a single conventional processor did in the both cases. Both methods are shown to have the same molecular structures and dynamics of the systems.     

Folding thermodynamics of PET-hydrolyzing enzyme Cut190 depending on Ca2+ concentration

The enzyme, cutinase from Saccharomonospora viridis AHK190 (Cut190), can hydrolyze the inner block of polyethylene terephthalate (PET). Cut190 has a unique feature that both its activity and thermal stability are increased upon Ca²⁺ binding. In consideration of the glass transition temperature of PET, which is between 60 and 65 °C, the increased activity and thermal stability are of great interest to apply for PET bio-recycling. Our previous mutational analysis showed that the S226P/R228S mutant (Cut190*) has a higher activity and thermal stability than those of the wild type. In this study, we analyzed the folding thermodynamics of the inactive mutant of Cut190*, Cut190*S176A, using circular dichroism and differential scanning calorimetry. The results show that the denaturation temperature increases from 54 to 71 °C due to the addition of 250 mM Ca²⁺, in a Ca²⁺ concentration-dependent manner. The increased thermal stability is mainly due to the increased enthalpy change, partially compensated by the increased entropy change. Based on the crystal structure of Cut190*S176A bound to Ca²⁺, molecular dynamics simulations were carried out to analyze the effects of Ca²⁺ on the structural dynamics, showing that the Ca²⁺-bound structure fluctuated less than the Ca²⁺-free structure. Structural analysis indicates that Ca²⁺ binding increases the intramolecular interactions of the enzyme, while decreasing its fluctuation, which are in good correlation with the experimental results of the folding thermodynamics.

     

Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water

Trivial trajectory parallelization of multicanonical molecular dynamics (TTP-McMD) explores the conformational space of a biological system with multiple short runs of McMD starting from various initial structures. This method simply connects (i.e., trivially parallelizes) the short trajectories and generates a long trajectory. First, we theoretically prove that the simple trajectory connection satisfies a detailed balance automatically. Thus, the resultant long trajectory is regarded as a single multicanonical trajectory. Second, we applied TTP-McMD to an alanine decapeptide with an all-atom model in explicit water to compute a free-energy landscape. The theory imposes two requirements on the multiple trajectories. We have demonstrated that TTP-McMD naturally satisfies the requirements. The TTP-McMD produces the free-energy landscape considerably faster than a single-run McMD does. We quantitatively showed that the accuracy of the computed landscape increases with increasing the number of multiple runs. Generally, the free-energy landscape of a large biological system is unknown a priori. The current method is suitable for conformational sampling of such a large system to reduce the waiting time to obtain a canonical ensemble statistically reliable.