Prediction of stability changes upon single-site mutations using database-derived potentials

One of the purposes of studying protein stability changes upon mutations is to get information about the dominating interactions that drive folding and stabilise the native structure. With this in mind, we present a method that predicts folding free-energy variations caused by point mutations using combinations of two types of database-derived potentials, i.e. backbone torsion-angle potentials and distance potentials, describing local and non-local interactions along the chain, respectively. The method is applied to evaluate the folding free-energy changes of 344 single-site mutations introduced in six different proteins and a synthetic peptide. We found that the relative importance of local versus non-local interactions along the chain is essentially a function of the solvent accessibility of the mutated residues. For the subset of totally buried residues, the optimal potential is the sum of a distance potential and a torsion potential weighted by a factor of 0.4. This combination yields a correlation coefficient between measured and computed changes in folding free energy of 0.80. For mutations of partially buried residues, the best potential is the sum of a torsion potential and a distance potential weighted by 0.7. For fully accessible residues, the torsion potentials taken alone perform best, reaching correlation coefficients of 0.87 on all but 10 mutations; the excluded mutations seem to modify the backbone structure or to involve interactions that are atypical for the surface. These results show that the relative weight of non-local interactions along the sequence decreases as the solvent accessibility of the mutated residue increases, and vanishes at the protein surface. On the contrary, the weight of local interactions increases with solvent accessibility. The latter interactions are nevertheless never negligible, even for the most buried residues. Received: 20 May 1998 / Accepted: 3 September 1998 / Published online: 7 December 1998     

Computational screening of biomolecular adsorption and self‐assembly on nanoscale surfaces

The quantification of binding properties of ions, surfactants, biopolymers, and other macromolecules to nanometer‐scale surfaces is often difficult experimentally and a recurring challenge in molecular simulation. A simple and computationally efficient method is introduced to compute quantitatively the energy of adsorption of solute molecules on a given surface. Highly accurate summation of Coulomb energies as well as precise control of temperature and pressure is required to extract the small energy differences in complex environments characterized by a large total energy. The method involves the simulation of four systems, the surface‐solute–solvent system, the solute–solvent system, the solvent system, and the surface‐solvent system under consideration of equal molecular volumes of each component under NVT conditions using standard molecular dynamics or Monte Carlo algorithms. Particularly in chemically detailed systems including thousands of explicit solvent molecules and specific concentrations of ions and organic solutes, the method takes into account the effect of complex nonbond interactions and rotational isomeric states on the adsorption behavior on surfaces. As a numerical example, the adsorption of a dodecapeptide on the Au {111} and mica {001} surfaces is described in aqueous solution. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

A new approach to analysis and display of local lipophilicity/hydrophilicity mapped on molecular surfaces

Summary A new method for display and analysis of lipophilic/hydrophilic properties on molecular surfaces is presented. The present approach is based on the concept of Crippen and coworkers that the overall hydrophobicity of a molecule (measured as the logarithm of the partition coefficient in an octanol/water system) can be obtained as a superposition of single atom contributions. It is also based on the concept of molecular lipophilicity potentials (MLP) first introduced by Audry and coworkers in order to establish a 3D lipophilicity potential profile in the molecular environment. Instead of using a l/r- or an exponential distance law between the atomic coordinates and a point on the molecular surface, a new distance dependency is introduced for the calculation of an MLP-value on the solvent-accessible surface of the molecule. In the present formalism the Crippen values (introduced for atoms in their characteristic structural environment) are projected onto the van der Waals surface of the molecule by a special weighting procedure. This guarantees that only those atomic fragments contribute significantly to the surface values that are in the close neighbourhood of the surface point. This procedure not only works for small molecules but also allows the characterization of the surfaces of biological macromolecules by means of local lipophilicity. Lipophilic and hydrophilic domains can be recognized by visual inspection of computer-generated images or by computational procedures using fuzzy logic strategies. Local hydrophobicities on different molecular surfaces can be quantitatively compared on the basis of the present approach.     

A consensus procedure improving solvent accessibility prediction

Prediction methods of structural features in 1D represent a useful tool for the understanding of folding, classification, and function of proteins, and, in particular, for 3D structure prediction. Among the structural aspects characterizing a protein, solvent accessibility has received great attention in recent years. The available methods proposed for predicting accessibility have never considered the combination of the results deriving from different methods to construct a consensus prediction able to provide more reliable results. A consensus approach that increases prediction accuracy using three high-performance methods is described. The results of our method for three different protein data sets show that up to 3.0% improvement in prediction accuracy of solvent accessibility may be obtained by a consensus approach. The improvement also extends to the correlation coefficient. Application of our consensus approach to the accessibility prediction using only three prediction methods gives results better than single methods combined for consensus formation. Currently, the scarce availability of predictors with similar parameters defining solvent accessibility hinders the testing of other methods in our consensus procedure.     

Instant Controlled Pressure Drop technology: From a new fundamental approach of instantaneous transitory thermodynamics to large industrial applications on high performance–high controlled quality unit operations

Solvent extraction processes have been largely used in various industries. They recently were improved through new physical concepts such as CO₂ Supercritical Fluid Extraction, Ultrasound assisted process, Microwave-assisted extraction, Instant Controlled Pressure Drop DIC-assisted extraction… Systematically, a pretreatment stage of grinding takes place in order to improve the exchange surface increasing the starting accessibility. Swelling of the material structure implies an increase of the porosity thus leading to higher solvent diffusivity within the solid matrix. A new concept of expanded granule powder has recently been defined using Instant Controlled Pressure Drop DIC technology. Whatever the type of solvent is (even CO₂-SFE), such a swelled structure dramatically intensifies the kinetics through a higher specific exchange surface thanks to the open pores, while improving the solution solvent–solute diffusivity within the solid. Coupled to ultrasound, the internal transfer of solute within the pore solvent can likewise be intensified by replacing molecular diffusion within the pores by an effective convection transfer. In this work, we carried out a first approach of modeling of solvent extraction kinetics of expanded granules involving higher exchange surface and greater internal diffusion process.     

Molecular dynamics simulations of sorption of organic compounds at the clay mineral/aqueous solution interface

The adsorption of trichloroethene, C₂HCl₃, on clay mineral surfaces in the presence of water has been modeled as an example describing a general program that uses molecular dynamics simulations to study the sorption of organic materials at the clay mineral/aqueous solution interface. Surfaces of the clay minerals kaolinite and pyrophyllite were hydrated at different water levels corresponding to partial and complete monolayers of water. In agreement with experimental trends, water was found to outcompete C₂HCl₃ for clay surface sites. The simulations suggest that at least three distinct mechanisms coexist for C₂HCl₃ on clay minerals in the environment. The most stable interaction of C₂HCl₃ with clay surfaces is by full molecular contact, coplanar with the basal surface. This kind of interaction is suppressed by increasing water loads. A second less stable and more reversible interaction involves adsorption through single-atom contact between one Cl atom and the surface. In a third mechanism, adsorbed C₂HCl₃ never contacts the clay directly but sorbs onto the first water layer. To test the efficacy of existing force field parameters of organic compounds in solid state simulations, molecular dynamics simulations of several representative organic crystals were also performed and compared with the experimental crystal structures. These investigations show that, in general, in condensed-phase studies, parameter evaluations are realistic only when thermal motion effects are included in the simulations. For chlorohydrocarbons in particular, further explorations are needed of atomic point charge assignments. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 144–153, 1998     

New approach for representation of molecular surface

A new algorithm is proposed for approximation to the molecular surface. It starts with a triangular mesh built on an ellipsoid embracing the whole molecular surface. The triangular mesh is obtained from an icosahedron subdivision sphere with highly uniform vertex distribution, and the embracing surface is deflated stepwise to the best adherence of its triangles onto the surface of the molecule. The deflating direction of each vertex of a triangle is defined by the vector normal at this point to the previous deflated embracing surface. Our results show that the speed of the triangulation embracing ellipsoid method and the quality of the surface obtained by the method are faster and better than the method that starts with a quadrilateral mesh built from meridian and parallel representations on an embracing sphere to get the molecular surface. Furthermore, the surface obtained by the method can be used directly to approximate the molecular surface by spherical harmonic expansions. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1805–1815, 1998     

The Conformations of Amino Acids on a Gold(111) Surface

The interactions of amino acids with inorganic surfaces are of interest for biologists and biotechnologists alike. However, the structural determinants of peptide–surface interactions have remained elusive, but are important for a structural understanding of the interactions of biomolecules with gold surfaces. Molecular dynamics simulations are a tool to analyze structures of amino acids on surfaces. However, such an approach is challenging due to lacking parameterization for many surfaces and the polarizability of metal surfaces. Herein, we report DFT calculations of amino acid fragments in vacuo and molecular dynamics simulations of the interaction of all amino acids with a gold(111) surface in explicit solvent, using the recently introduced polarizable gold force field GolP. We describe preferred orientations of the amino acids on the metal surface. We find that all amino acids preferably interact with the gold surface at least partially with their backbone, underlining an unfolding propensity of gold surfaces.     

Dimensionality of amino acid space and solvent accessibility prediction with neural networks

Solvent accessibility prediction from amino acid sequences has been pursued by several researchers. Such a prediction typically starts by transforming the amino acid category (or type) information into numerical representations. All twenty amino acids can be completely and uniquely represented by 20-dimensional vectors. Here, we investigate if the amino acid space defined in this way really requires twenty dimensions. We tried to develop corresponding representations in fewer dimensions. A method for searching optimal codification schema in an arbitrary space using neural networks was developed. The method is used to obtain optimal encoding of amino acids at various levels of dimensionality, and applied to optimize the amino acid codifications for the prediction of the solvent accessibility values of the proteins using feed-forward neural networks. The traditional 20-dimensional codification seems to be redundant in solving the solvent accessibility prediction problem, since a 1-dimensional codification is able to achieve almost the same degree of accuracy as the 20-dimensional codification. Optimal coding in much fewer dimensions could be used to make the predictions of accessible surface area with almost the same degree of accuracy as that obtained by a fully unique 20-dimensional coding. The 1-dimensional amino acid codification for solvent accessibility prediction obtained by a purely mathematical way based on neural networks is highly correlated with a physical property of the amino acids, namely their average solvent accessibility. The method developed to find the optimal codification is general, although the codification thus produced is dependent on the type of estimated property.     

A generalized Langevin dynamics approach to model solvent dynamics effects on proteins via a solvent-accessible surface. The carboxypeptidase A inhibitor protein as a model

A generalized Langevin dynamics (GLD) scheme is derived for (bio)macromolecules having internal structure, arbitrary shapes and a size larger than solvent molecules (i.e. proteins). The concept of solvent-accessible surface area (SASA) is used to incorporate solvent effects via external forces thereby avoiding its explicit molecular representation. A simulation algorithm is implemented in the GROMOS molecular dynamics (MD) program including random forces and memory effects, while solvation effects enter via derivatives of the surface area. The potato carboxypeptidase inhibitor (PCI), a small protein, is used to numerically test the approach. This molecule has N- and C-terminal tails whose structure and fluctuations are solvent dependent. A 1-ns MD trajectory was analyzed in depth. X-ray and NMR structures are used in conjunction with MD simulations with and without explicit solvent to gauge the quality of the results. All the analyses showed that the GLD simulation approached the results obtained for the MD simulation with explicit simple-point-charge-model water molecules. The SASAs of the polar atoms show a natural exposure towards the solvent direction. A FLS solvent simulation was completed in order to sense memory effects. The approach and results presented here could be of great value for developing alternatives to the use of explicit solvent molecules in the MD simulation of proteins, expanding its use and the time-scale explored. Received: 2 February 2000 / Revised: 12 March 2000 / Accepted: 26 May 2000 / Published online: 2 November 2000     

Solvent-controlled organization of self-assembled polymeric monolayers on gold: an easy approach for the construction of protein resistant surfaces

Protein resistant surfaces based on poly(ethylene glycol) (PEG) coatings are extensively applied in the fields of biosensors, tissue engineering, fundamental cell-surface interaction research, and drug delivery systems. The structural organization of the PEG film on the surface has a significant effect on the performance of the film to resist protein adsorption. In this paper, we report an approach using solvent to control the organization of the polymeric monolayer on gold. A water soluble copolymer with grafted PEG side chains and alkyl disulfide side chains was synthesized. A polymeric monolayer was fabricated on a gold surface from different solutions (water- and toluene-based) of the copolymer. The organization of the polymeric monolayers was characterized by means of ellipsometry, cyclic voltammetry, contact angle, X-ray photoelectron spectroscopy, and atomic force microscopy. It was proven that the structural organization of the polymeric monolayer on a gold surface could be controlled by the solvent. A polymeric monolayer with PEG enriched at the outer level is obtained when water is used as the solvent. Various types of proteins, including fibrinogen, albumin, and normal human serum, were used to test the protein resistance of the gold surfaces modified by the polymeric monolayers. The polymeric monolayer formed from a water solution of the copolymer showed excellent protein resistance. In addition, by using water as the solvent, patterning of the polymeric monolayer could easily be achieved through a combination of lift-off and self-assembly. We believe that the approach reported here provides an easy, fast, and efficient way to fabricate a robust protein resistant surface.     

Hydroxyl radical probe of the surface of lysozyme by synchrotron radiolysis and mass spectrometry.

A new approach is reported that combines synchrotron radiolysis and mass spectrometry to probe the surface of proteins. Hydroxyl radicals produced upon the radiolysis of protein solutions with synchrotron light for several milliseconds result in the reaction of amino acid side chains. This results in the formation of stable oxidation products where the level of oxidation at the reactive residues is influenced by the accessibility of their side chains to the bulk solvent. The aromatic and sulfur-containing residues have been found to react preferentially in accord with previous peptide studies. The sites of oxidation have been determined by tandem mass spectrometry. The rate of oxidation at these reactive markers has been measured for each of the proteolytic peptides as a function of exposure time based on the relative proportion of modified and unmodified peptide ions detected by mass spectrometry. Oxidation rates have been found to correlate closely with a theoretical measure of the accessibility of residue side chains to the bulk solvent in the native protein structure. The synchrotron-based approach is able to distinguish the relative accessibility of the tryptophan residue side chains of lysozyme at positions 62 and 123 from each other and all other tryptophan residues based on their rates of oxidation.     

Microscopic models for quantum mechanical calculations of chemical processes in solutions: LD/AMPAC and SCAAS/AMPAC calculations of solvation energies

Our previously developed approaches for integrating quantum mechanical molecular orbital methods with microscopic solvent models are refined and examined. These approaches consider the nonlinear solute–solvent coupling in a self-consistent way by incorporating the potential from the solvent dipoles in the solute Hamiltonian, while considering the polarization of the solvent by the potential from the solute charges. The solvent models used include the simplified Langevin Dipoles (LD) model and the much more expensive surface constrained All Atom Solvent (SCAAS) model, which is combined with a free energy pertubation (FEP) approach. Both methods are effectively integrated with the quantum mechanical AMPAC package and can be easily combined with other quantum mechanical programs. The advantages of the present approaches and their earlier versions over macroscopic reaction field models and supermolecular approaches are considered. A LD/MNDO study of solvated organic ions demonstrates that this model can yield reliable solvation energies, provided the quantum mechanical charges are scaled to have similar magnitudes to those obtained by high level ab initio methods. The incorporation of a field-dependent hydrophobic term in the LD free energy makes the present approach capable of evaluating the free energy of transfer of polar molecules from non polar solvents to aqueous solutions. The reliability of the LD approach is examined not only by evaluating a rather standard set of solvation energies of organic ions and polar molecules, but also by considering the stringent test case of sterically hindered hydrophobic ions. In this case, we compare the LD/MNDO solvation energies to the more rigorous FEP/SCAAS/MNDO solvation energies. Both methods are found to give similar results even in this challenging test case. The FEP/SCAAS/AMPAC method is incorporated into the current version of the program ENZYMIX. This option allows one to study chemical reactions in enzymes and in solutions using the MNDO and AM1 approximations. A special procedure that uses the EVB method as a reference potential for SCF MO calculations should help in improving the reliability of such studies.     

Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues

Relative amino acid residue solvent accessibility values allow the quantitative comparison of atomic solvent-accessible surface areas in different residue types and physical environments in proteins and in protein structural alignments. Geometry-optimised tri-peptide structures in extended solvent-exposed reference conformations have been obtained for 43 amino acid residue types at a high level of quantum chemical theory. Significant increases in side-chain solvent accessibility, offset by reductions in main-chain atom solvent exposure, were observed for standard residue types in partially geometry-optimised structures when compared to non-minimised models built from identical sets of proper dihedral angles abstracted from the literature. Optimisation of proper dihedral angles led most notably to marked increases of up to 54% in proline main-chain atom solvent accessibility compared to literature values. Similar effects were observed for fully-optimised tri-peptides in implicit solvent. The relief of internal strain energy was associated with systematic variation in N, C^α and C^β atom solvent accessibility across all standard residue types. The results underline the importance of optimisation of ‘hard’ degrees of freedom (bond lengths and valence bond angles) and improper dihedral angle values from force field or other context-independent reference values, and impact on the use of standardised fixed internal co-ordinate geometry in sampling approaches to the determination of absolute values of protein amino acid residue solvent accessibility. Quantum chemical methods provide a useful and accurate alternative to molecular mechanics methods to perform energy minimisation of peptides containing non-standard (chemically modified) amino acid residues frequently present in experimental protein structure data sets, for which force field parameters may not be available. Reference tri-peptide atomic co-ordinate sets including hydrogen atoms are made freely available.     

A facile method for preparing sticky, hydrophobic polymer surfaces

Textured surfaces consisting of nanometer- to micrometer-sized lightly sulfonated polystyrene ionomer (SPS) particles were prepared by rapid evaporation of the solvent from a dilute polymer solution-cast onto silica. The particle textured ionomer surfaces were prepared by either spin-coating or solution-casting ionomer solutions at controlled evaporation rates. The effects of the solvent used to spin-coat the film, the molecular weight of the ionomer, and the rate of solvent evaporation on the surface morphology of cast films were investigated. The surface morphologies were consistent with a spinodal decomposition mechanism, where the surface first existed as a percolated-like structure and then ripened into droplets if molecular mobility was retained for sufficient time. The SPS particles or particle aggregates were robust and resisted separation from the surface even after annealing at 120 °C for 1 week. The water contact angles on as-prepared surfaces were relatively low, ～90°, due to the polar groups in the ionomer, but when the surface was modified by chemical vapor deposition of 1H,1H,2H,2H-perfluorooctyltrichlorosilane, the surface contact angles increased to ～109° on smooth surfaces and up to ～140° on the textured surfaces. Although the surfaces were hydrophobic, the contact angle hysteresis was relatively high and water droplets stuck to these surfaces even when the surface was turned upside down.     

How accurate can molecular dynamics/linear response and Poisson–Boltzmann/solvent accessible surface calculations be for predicting relative binding affinities? Acetylcholinesterase huprine inhibitors as a test case

This study examines the accuracy of molecular dynamics-linear response (MD/LR) and Poisson–Boltzmann/solvent accessible surface (PB/SAS) calculations to predict relative binding affinities. A series of acetylcholinesterase (AChE) huprine inhibitors has been chosen as a test system owing to the availability of free-energy (thermodynamic integration) calculations. The results obtained with the MD/LR approach point out a clear relationship between the experimental affinity and the electrostatic interaction energy alone for a subset of huprines, but the suitability of the MD/LR approach to predict the binding affinity of the whole series of compounds is limited. On the other hand, PB/SAS calculations show a marked dependence on both the computational protocol and the nature of the inhibitor–enzyme complex. Received: 2 August 2000 / Accepted: 8 September 2000 / Published online: 21 December 2000