Minimalist explicit solvation models for surface loops in proteins

We have performed molecular dynamics simulations of protein surface loops solvated by explicit water, where a prime focus of the study is the small numbers (e.g., ~100) of explicit water molecules employed. The models include only part of the protein (typically 500 - 1000 atoms), and the water molecules are restricted to a region surrounding the loop. In this study, the number of water molecules (N(w)) is systematically varied, and convergence with large N(w) is monitored to reveal N(w)(min), the minimum number required for the loop to exhibit realistic (fully hydrated) behavior. We have also studied protein surface coverage, as well as diffusion and residence times for water molecules as a function of N(w). A number of other modeling parameters are also tested. These include the number of environmental protein atoms explicitly considered in the model, as well as two ways to constrain the water molecules to the vicinity of the loop (where we find one of these methods to perform better when N(w) is small). The results (for RMSD and its fluctuations for four loops) are further compared to much larger, fully solvated systems (using ~10,000 water molecules under periodic boundary conditions and Ewald electrostatics), and to results for the GBSA implicit solvation model. We find that the loop backbone can stabilize with a surprisingly small number of water molecules (as low as 5 molecules per amino acid residue). The side chains of the loop require somewhat larger N(w), where the atomic fluctuations become too small if N(w) is further reduced. Thus, in general, we find adequate hydration to occur at roughly 12 water molecules per residue. This is an important result, because at this hydration level, computational times are comparable to those required for GBSA. Therefore these "minimalist explicit models" can provide a viable and potentially more accurate alternative. The importance of protein loop modeling is discussed in the context of these, and other, loop models, along with other challenges including the relevance of appropriate free energy simulation methodology for assessment of conformational stability.     

Chemically resolved photovoltage measurements in CdSe nanoparticle films

Light-induced chemically resolved electrical measurements (CREM) under controlled electrical conditions are used to study photovoltaic effects at selected regions in nanocrystalline CdSe-based films. The method, based on X-ray photoelectron spectroscopy (XPS), possesses unique capabilities for exploring charge trapping and charge transport mechanisms, combining spectrally filtered input signals with photocurrent detection and with a powerful, site-selective, photovoltage probe.     

Multicanonical procedure for continuum peptide models

The multicanonical (Muca) Monte Carlo method enables simulating a system over a wide range of temperatures and thus has become an efficient tool for studying spin glasses, first‐order phase transitions, the helix–coil transition of polypeptides, and protein folding. However, implementation of the method requires calculating the multicanonical weights by an iterative procedure that is not straightforward and is a stumbling block for newcomers. A recursive procedure that takes into account the statistical errors of all previous iterations and thus enables an automatic calculation of the weights without the need for human intervention after each iteration has been proposed. This procedure, which has already been tested successfully for lattice systems, is extended here to continuum models of peptides and proteins. The method is examined in detail and tested for models of the pentapeptide Leu‐enkephalin (Tyr‐Gly‐Gly‐Phe‐Leu) described by the potential energy function ECEPP. Because of the great interest in the structural mapping of the low‐energy region of biomolecules, the energy of structures selected from the Muca trajectory is minimized. The extent of conformational coverage provided by the method is examined and found to be very satisfactory. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1251–1261, 2000     

The role played by oxygen plasma on Teflon: relevance to the concept of "cryptoelectrons"

Dr Williams (AIP Adv., 2012, 2, 010701) suggested that cleaning Teflon by high pressure oxygen plasma may have affected our result that Cu(2+) and Pd(2+) ions can be absorbed but not chemically reduced by a Teflon surface rubbed by PMMA (Phys. Chem. Chem. Phys., 2012, 14, 5551). In response, we show that this treatment does not affect the adsorption of Cu(2+) and Pd(2+). We reaffirm our statement that Cu(2+) and Pd(2+) ions can be adsorbed by a Teflon surface only after rubbing with the organic polymers, not before rubbing.     

Molecular length, monolayer density, and charge transport: lessons from Al-AlOx/alkyl-phosphonate/Hg junctions

A combined electronic transport-structure characterization of self-assembled monolayers (MLs) of alkyl-phosphonate (AP) chains on Al-AlOx substrates indicates a strong molecular structural effect on charge transport. On the basis of X-ray reflectivity, XPS, and FTIR data, we conclude that "long" APs (C14 and C16) form much denser MLs than do "short" APs (C8, C10, C12). While current through all junctions showed a tunneling-like exponential length-attenuation, junctions with sparsely packed "short" AP MLs attenuate the current relatively more efficiently than those with densely packed, "long" ones. Furthermore, "long" AP ML junctions showed strong bias variation of the length decay coefficient, β, while for "short" AP ML junctions β is nearly independent of bias. Therefore, even for these simple molecular systems made up of what are considered to be inert molecules, the tunneling distance cannot be varied independently of other electrical properties, as is commonly assumed.     

Coordination-based gold nanoparticle layers

Gold nanoparticle (NP) mono- and multilayers were constructed on gold surfaces using coordination chemistry. Hydrophilic Au NPs (6.4 nm average core diameter), capped with a monolayer of 6-mercaptohexanol, were modified by partial substitution of bishydroxamic acid disulfide ligand molecules into their capping layer. A monolayer of the ligand-modified Au NPs was assembled via coordination with Zr4+ ions onto a semitransparent Au substrate (15 nm Au, evaporated on silanized glass and annealed) precoated with a self-assembled monolayer of the bishydroxamate disulfide ligand. Layer-by-layer construction of NP multilayers was achieved by alternate binding of Zr4+ ions and ligand-modified NPs onto the first NP layer. Characterization by atomic force microscopy (AFM), ellipsometry, wettability, transmission UV-vis spectroscopy, and cross-sectional transmission electron microscopy showed regular growth of NP layers, with a similar NP density in successive layers and gradually increased roughness. The use of coordination chemistry enables convenient step-by-step assembly of different ligand-possessing components to obtain elaborate structures. This is demonstrated by introducing nanometer-scale vertical spacing between a NP layer and the gold surface, using a coordination-based organic multilayer. Electrical characterization of the NP films was carried out using conductive AFM, emphasizing the barrier properties of the organic spacer multilayer. The results exhibit the potential of coordination self-assembly in achieving highly controlled composite nanostructures comprising molecules, NPs, and other ligand-derivatized components.     

Calculation of the entropy and free energy from monte carlo simulations of a peptide stretched by an external force

Hypothetical scanning Monte Carlo (HSMC) is a method for calculating the absolute entropy, S, and free energy, F, from a trajectory generated by any simulation technique. HSMC was applied initially to fluids (argon and water) and later to peptides and self-avoiding walks on a lattice. In this paper we make a step further and apply it to a model of decaglycine (at T = 300 K) in vacuum with constant bond lengths where external stretching forces are exerted at the end points; the changes in S and F are calculated as the forces are increased. The molecule is placed initially in a helical structure, which is changed to an extended structure after a short simulation time due to the exerted forces. This study has relevance to problems in polymers (e.g., rubber elasticity) and to the analysis of experiments where individual molecules are stretched by atomic force microscopy (AFM), for example. The results for S and F are accurate and are significantly better than those obtained by the quasi-harmonic approximation and the local states method. However, the molecule is quite stiff due to the strong bond angle potentials and the extensions are small even for relatively large forces. Correspondingly, as the force is increased the decrease in the entropy is relatively small while the potential energy is enhanced significantly. Still, differences, TDeltaS, for different forces are obtained with very good accuracy of approximately 0.2 kcal/mol.     

Calculation of the entropy of random coil polymers with the hypothetical scanning Monte Carlo method

Hypothetical scanning Monte Carlo (HSMC) is a method for calculating the absolute entropy S and free energy F from a given MC trajectory developed recently and applied to liquid argon, TIP3P water, and peptides. In this paper HSMC is extended to random coil polymers by applying it to self-avoiding walks on a square lattice--a simple but difficult model due to strong excluded volume interactions. With HSMC the probability of a given chain is obtained as a product of transition probabilities calculated for each bond by MC simulations and a counting formula. This probability is exact in the sense that it is based on all the interactions of the system and the only approximation is due to finite sampling. The method provides rigorous upper and lower bounds for F, which can be obtained from a very small sample and even from a single chain conformation. HSMC is independent of existing techniques and thus constitutes an independent research tool. The HSMC results are compared to those obtained by other methods, and its application to complex lattice chain models is discussed; we emphasize its ability to treat any type of boundary conditions for which a reference state (with known free energy) might be difficult to define for a thermodynamic integration process. Finally, we stress that the capability of HSMC to extract the absolute entropy from a given sample is important for studying relaxation processes, such as protein folding.     

On the zero fluctuation of the “microscopic free energy” and its potential use

The fluctuations of the microscopic free energy calculated with the ensemble probability are shown to be zero. We suggest that this result be used for estimating approximate free energies calculated on the basis of the minimum free energy principle. As an example the estimation is performed with respect to a certain computer simulation of the square Ising lattice. The zero fluctuations also can be used to obtain relations among fluctuations with the accurate ensemble probability distribution.