A convective replica‐exchange method for sampling new energy basins

Replica‐exchange is a powerful simulation method for sampling the basins of a rugged energy landscape. The replica‐exchange method's sampling is efficient because it allows replicas to perform round trips in temperature space, thereby visiting both low and high temperatures in the same simulation. However, replicas have a diffusive walk in temperature space, and the round trip rate decreases significantly with the system size. These drawbacks make convergence of the simulation even more difficult than it already is when bigger systems are tackled. Here, we present a simple modification of the exchange method. In this method, one of the replicas steadily raises or lowers its temperature. We tested the convective replica‐exchange method on three systems of varying complexity: the alanine dipeptide in implicit solvent, the GB1 β‐hairpin in explicit solvent and the Aβ_25–35 homotrimer in a coarse grained representation. For the highly frustrated Aβ_25–35 homotrimer, the proposed “convective” replica‐exchange method is twice as fast as the standard method. It discovered 24 out of 27 free‐energy basins in less than 500 ns. It also prevented the formation of groups of replicas that usually form on either side of an exchange bottleneck, leading to a more efficient sampling of new energy basins than in the standard method. © 2012 Wiley Periodicals, Inc.     

Coulomb replica‐exchange method: Handling electrostatic attractive and repulsive forces for biomolecules

We propose a new type of the Hamiltonian replica‐exchange method (REM) for molecular dynamics (MD) and Monte Carlo simulations, which we refer to as the Coulomb REM (CREM). In this method, electrostatic charge parameters in the Coulomb interactions are exchanged among replicas while temperatures are exchanged in the usual REM. By varying the atom charges, the CREM overcomes free‐energy barriers and realizes more efficient sampling in the conformational space than the REM. Furthermore, this method requires only a smaller number of replicas because only the atom charges of solute molecules are used as exchanged parameters. We performed Coulomb replica‐exchange MD simulations of an alanine dipeptide in explicit water solvent and compared the results with those of the conventional canonical, replica exchange, and van der Waals REMs. Two force fields of AMBER parm99 and AMBER parm99SB were used. As a result, the CREM sampled all local‐minimum free‐energy states more frequently than the other methods for both force fields. Moreover, the Coulomb, van der Waals, and usual REMs were applied to a fragment of an amyloid‐β peptide (Aβ) in explicit water solvent to compare the sampling efficiency of these methods for a larger system. The CREM sampled structures of the Aβ fragment more efficiently than the other methods. We obtained β‐helix, α‐helix, 3₁₀‐helix, β‐hairpin, and β‐sheet structures as stable structures and deduced pathways of conformational transitions among these structures from a free‐energy landscape. © 2012 Wiley Periodicals, Inc.     

Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

We have developed a two‐dimensional replica‐exchange method for the prediction of protein–ligand binding structures. The first dimension is the umbrella sampling along the reaction coordinate, which is the distance between a protein binding pocket and a ligand. The second dimension is the solute tempering, in which the interaction between a ligand and a protein and water is weakened. The second dimension is introduced to make a ligand follow the umbrella potential more easily and enhance the binding events, which should improve the sampling efficiency. As test cases, we applied our method to two protein‐ligand complex systems (MDM2 and HSP 90‐alpha). Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank much faster with the improved sampling efficiency than the replica‐exchange umbrella sampling method that we have previously developed. © 2013 Wiley Periodicals, Inc.     

Multidimensional umbrella sampling and replica‐exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers

Structural information of a transmembrane (TM) helix dimer is useful in understanding molecular mechanisms of important biological phenomena such as signal transduction across the cell membrane. Here, we describe an umbrella sampling (US) scheme for predicting the structure of a TM helix dimer in implicit membrane using the interhelical crossing angle and the TM–TM relative rotation angles as the reaction coordinates. This scheme conducts an efficient conformational search on TM–TM contact interfaces, and its robustness is tested by predicting the structures of glycophorin A (GpA) and receptor tyrosine kinase EphA1 (EphA1) TM dimers. The nuclear magnetic resonance (NMR) structures of both proteins correspond to the global free‐energy minimum states in their free‐energy landscapes. In addition, using the landscape of GpA as a reference, we also examine the protocols of temperature replica‐exchange molecular dynamics (REMD) simulations for structure prediction of TM helix dimers in implicit membrane. A wide temperature range in REMD simulations, for example, 250–1000 K, is required to efficiently obtain a free‐energy landscape consistent with the US simulations. The interhelical crossing angle and the TM–TM relative rotation angles can be used as reaction coordinates in multidimensional US and be good measures for conformational sampling of REMD simulations. © 2013 Wiley Periodicals, Inc.     

Hamiltonian replica‐exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles

A Hamiltonian Replica‐Exchange Molecular Dynamics (REMD) simulation method has been developed that employs a two‐dimensional backbone and one‐dimensional side chain biasing potential specifically to promote conformational transitions in peptides. To exploit the replica framework optimally, the level of the biasing potential in each replica was appropriately adapted during the simulations. This resulted in both high exchange rates between neighboring replicas and improved occupancy/flow of all conformers in each replica. The performance of the approach was tested on several peptide and protein systems and compared with regular MD simulations and previous REMD studies. Improved sampling of relevant conformational states was observed for unrestrained protein and peptide folding simulations as well as for refinement of a loop structure with restricted mobility of loop flanking protein regions. © 2013 Wiley Periodicals, Inc.     

A new linear method for analyzing four‐way multiblock tables: STATIS‐4

A new four‐way multiblock method is proposed to study the links between more than two sets of data tables (several multiblocks) measured on the same observations. This method, called STATIS‐4, generalizes the STATIS method to more than one set of matrices. In its first step, STATIS‐4 is searching for one consensus for each multiblock and a global consensus summarizing all the previous ones as good as possible. Some graphical representations can be made to visualize the proximities between the tables within a multiblock and to visualize those between all the multiblocks. Moreover, plots of the observations for each table, each multiblock and global observations can be made. The theory of STATIS‐4 and the algorithm used to obtain the optimal solutions are presented. Moreover, a real sensory dataset is studied with STATIS‐4. Copyright © 2008 John Wiley & Sons, Ltd.     

Depurated inversion method for orbital‐specific exchange potentials

This work presents exchange potentials for specific orbitals calculated by inverting Hartree–Fock wavefunctions. This was achieved by using a Depurated Inversion Method. The basic idea of the method relies on the substitution of Hartree–Fock orbitals and eigenvalues into the Kohn–Sham equation. Through inversion, the corresponding effective potentials were obtained. Further treatment of the inverted potential should be carried on. The depuration is a careful optimization which eliminates the poles and also ensures the fullfilment of the appropriate boundary conditions. The procedure developed here is not restricted to the ground state or to a nodeless orbital and is applicable to all kinds of atoms. As an example, exchange potentials for noble gases and term‐dependent orbitals of the lower configuration of Nitrogen are calculated. The method allows to reproduce the input energies and wavefunctions with a remarkable degree of accuracy.     

Virtual‐system‐coupled adaptive umbrella sampling to compute free‐energy landscape for flexible molecular docking

A novel enhanced conformational sampling method, virtual‐system‐coupled adaptive umbrella sampling (V‐AUS), was proposed to compute 300‐K free‐energy landscape for flexible molecular docking, where a virtual degrees of freedom was introduced to control the sampling. This degree of freedom interacts with the biomolecular system. V‐AUS was applied to complex formation of two disordered amyloid‐β (Aβ_30–35) peptides in a periodic box filled by an explicit solvent. An interpeptide distance was defined as the reaction coordinate, along which sampling was enhanced. A uniform conformational distribution was obtained covering a wide interpeptide distance ranging from the bound to unbound states. The 300‐K free‐energy landscape was characterized by thermodynamically stable basins of antiparallel and parallel β‐sheet complexes and some other complex forms. Helices were frequently observed, when the two peptides contacted loosely or fluctuated freely without interpeptide contacts. We observed that V‐AUS converged to uniform distribution more effectively than conventional AUS sampling did. © 2015 Wiley Periodicals, Inc.     

Assembled cation‐exchange/anion‐exchange polypyrrole layers as new simplified artificial muscles

A simplified artificial muscle has been constructed by assembling different polypyrrole structures in the same synthesis process. This produces not only “all‐polymeric” but rather a new generation of “all‐conducting‐polymer” artificial muscles, capable of moving in electrolytic media by an electrical current application with no evidence of delamination after several cycles. Suitable devices can be constructed for biomedical applications, based on this conducting polymer film. Copyright © 2006 John Wiley & Sons, Ltd.     

SnifProbe: new method and device for vapor and gas sampling

SnifProbe is based on the use of 15 mm short pieces of standard 0.53 mm I.D. capillary or porous layer open tubular columns for sampling airborne, headspace, aroma or air pollution samples. A miniaturized frit-bottomed packed vial named MicroSPE was also prepared which served for the sampling of solvent vapors and gases as well as liquid water. The short (15 mm) trapping column is inserted into the SnifProbe easy-insertion-port and the SnifProbe is located or aimed at the sample environment. A miniature pump is operated for pumping 10-60 ml/min of the air sample through the short piece of column to collect the sample. After a few seconds up to a few minutes of pumping, the short column is removed from the SnifProbe with tweezers (or gloved hands) and placed inside a glass vial of a direct sample introduction device (ChromatoProbe) having a 0.5 mm hole at its bottom. The ChromatoProbe sample holder with its glass vial and sample in the short column are introduced into the GC injector as usual. The sample is then quickly and efficiently desorbed from the short sample column and is transferred into the analytical column for conventional GC and/or GC-MS analysis. We have explored the various characteristics of SnifProbe and demonstrated its applicability and effectiveness in many applications. These applications include: the analysis of benzene, toluene and o-xylene in air, SO2 in air, perfume aroma on hand, beer headspace, wine aroma, coffee aroma, cigarette smoke, trace chemical warfare agent simulants, explosives vapors, ethanol in human breath and odorants in domestic cooking gas. SnifProbe can be operated in the field or at a chemical process. The sample columns can be plugged and stored in a small union storage device, placed in a small plastic bag, marked and brought to the laboratory for analysis with the full power of GC and/or GC-MS. Accordingly, we feel that the major and most significant feature of SnifProbe is that it brings the field and process to the laboratory. Thus, SnifProbe can extend the "arm" of the GC and GC-MS laboratory and enable high-quality field and process analysis.     

Free energy derivatives: A new method for probing the convergence problem in free energy calculations

The convergence behavior of free energy calculations has been explored in more detail than in any previously reported work, using a model system of two neon atoms in a periodic box of water. We find that for thermodynamic integration-type free energy calculations as much as a nanosecond or more molecular dynamics sampling is required to obtain a fully converged value for a single λ point of the integrand. The concept of “free energy derivatives” with respect to the individual parameters of the force field is introduced. This formalism allows the total convergence of the simulation to be deconvoluted into components. A determination of the statistical “sampling ratio” from these simulations indicates that for window-type free energy calculations carried out in a periodic waterbox of typical size at least 0.6 ps of sampling should be performed at each window (0.7 ps if constraint contributions to the free energy are being determined). General methods to estimate and reduce the error in thermodynamic integration and free energy perturbation calculations are discussed. We show that the difficulty in applying such methods is determining a reliable estimate of the correlation length from a short series of data. © 1994 by John Wiley & Sons, Inc.     

A new quantum method for electrostatic solvation energy of protein

A new method that incorporates the conductorlike polarizable continuum model (CPCM) with the recently developed molecular fractionation with conjugate caps (MFCC) approach is developed for ab initio calculation of electrostatic solvation energy of protein. The application of the MFCC method makes it practical to apply CPCM to calculate electrostatic solvation energy of protein or other macromolecules in solution. In this MFCC-CPCM method, calculation of protein solvation is divided into calculations of individual solvation energies of fragments (residues) embedded in a common cavity defined with respect to the entire protein. Besides computational efficiency, the current approach also provides additional information about contribution to protein solvation from specific fragments. Numerical studies are carried out to calculate solvation energies for a variety of peptides including alpha helices and beta sheets. Excellent agreement between the MFCC-CPCM result and those from the standard full system CPCM calculation is obtained. Finally, the MFCC-CPCM calculation is applied to several real proteins and the results are compared to classical molecular mechanics Poisson-Boltzmann (MM/PB) and quantum Divid-and-Conque Poisson-Boltzmann (D&C-PB) calculations. Large wave function distortion energy (solute polarization energy) is obtained from the quantum calculation which is missing in the classical calculation. The present study demonstrates that the MFCC-CPCM method is readily applicable to studying solvation of proteins.     

A new method for preparation of PS‐g‐PA6 grafted copolymer micelles

This work described a new method for the synthesis of PS‐g‐PA6 grafted copolymer micelles. PS‐g‐PA6 sphere micelles were synthesized by using a same solvent at the absence of selective solvent. The morphologies of micelles were characterized by SEM and TEM. The PS‐g‐PA6 micelles loaded Fe₃O₄ particles have better MRI imaging effect. The synthesis strategy developed here may present a desirable way to fabricate grafted copolymer micelles.     

A new method for the gradient‐based optimization of molecular complexes

We present a novel method for the local optimization of molecular complexes. This new approach is especially suited for usage in molecular docking. In molecular modeling, molecules are often described employing a compact representation to reduce the number of degrees of freedom. This compact representation is realized by fixing bond lengths and angles while permitting changes in translation, orientation, and selected dihedral angles. Gradient‐based energy minimization of molecular complexes using this representation suffers from well‐known singularities arising during the optimization process. We suggest an approach new in the field of structure optimization that allows to employ gradient‐based optimization algorithms for such a compact representation. We propose to use exponential mapping to define the molecular orientation which facilitates calculating the orientational gradient. To avoid singularities of this parametrization, the local minimization algorithm is modified to change efficiently the orientational parameters while preserving the molecular orientation, i.e. we perform well‐defined jumps on the objective function. Our approach is applicable to continuous, but not necessarily differentiable objective functions. We evaluated our new method by optimizing several ligands with an increasing number of internal degrees of freedom in the presence of large receptors. In comparison to the method of Solis and Wets in the challenging case of a non‐differentiable scoring function, our proposed method leads to substantially improved results in all test cases, i.e. we obtain better scores in fewer steps for all complexes. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009     

Hamiltonian replica‐permutation method and its applications to an alanine dipeptide and amyloid‐β(29–42) peptides

We propose the Hamiltonian replica‐permutation method (RPM) (or multidimensional RPM) for molecular dynamics and Monte Carlo simulations, in which parameters in the Hamiltonian are permuted among more than two replicas with the Suwa‐Todo algorithm. We apply the Coulomb RPM, which is one of realization of the Hamiltonian RPM, to an alanine dipeptide and to two amyloid‐β(29–42) molecules. The Hamiltonian RPM realizes more efficient sampling than the Hamiltonian replica‐exchange method. We illustrate the protein misfolding funnel of amyloid‐β(29–42) and reveal its dimerization pathways. © 2013 Wiley Periodicals, Inc.