Generating transition paths by Langevin bridges

We propose a novel stochastic method to generate paths conditioned to start in an initial state and end in a given final state during a certain time t(f). These paths are weighted with a probability given by the overdamped Langevin dynamics. We show that these paths can be exactly generated by a non-local stochastic differential equation. In the limit of short times, we show that this complicated non-solvable equation can be simplified into an approximate local stochastic differential equation. For longer times, the paths generated by this approximate equation do not satisfy the correct statistics, but this can be corrected by an adequate reweighting of the trajectories. In all cases, the paths are statistically independent and provide a representative sample of transition paths. The method is illustrated on the one-dimensional quartic oscillator.     

On the estimation of stability parameters from heat-induced conformational transition curves of proteins

A method is suggested to determine valid and authentic values of thermodynamic stability parameters of proteins from their heat-induced conformational transition curves. We show (a) that the estimate of ΔH_m ^van, the enthalpy change on denaturation at T_m, the midpoint of denaturation, is significantly less than ΔH_m ^cal, the value obtained by the calorimetric measurements, if the analysis of the conformational transition curve uses the conventional method which assumes a linear temperature-dependence of the pre- and post-transition baselines; and (b) that there exists an excellent agreement between ΔH_m ^van and ΔH_m ^cal values of proteins, if the analysis of thermal denaturation curves assumes that the temperature-dependence of pre- and post-transition baselines is described by a parabolic function. The latter analysis is supported by our observations that the temperaturedependencies of the absorption and circular dichroism properties of protein groups are indeed nonlinear. It is observed that the estimate of ΔC_p, the constant-pressure heat capacity change is independent of the model used to describe the temperaturedependence of the pre- and post-transition baselines. An important conclusion is that for proteins which exhibit a two-state character, all stability parameters are measured with the same error as that observed with a calorimeter.     

Using swarm intelligence for finding transition states and reaction paths

We describe an algorithm that explores potential energy surfaces (PES) and finds approximate reaction paths and transition states. A few (≈6) evolving atomic configurations ("climbers") start near a local minimum M1 of the PES. The climbers seek a shallow ascent, low energy, path toward a saddle point S12, cross over to another valley of the PES, and climb down to a new minimum M2 that was not known beforehand. Climbers use both energy and energy derivatives to make individual decisions, and they use relative fitness to make team-based decisions. In sufficiently long runs, they keep exploring and may go through a sequence M1-S12-M2-S23-M3 ... of minima and saddle points without revisiting any of the critical points. We report results on eight small test systems that highlight advantages and disadvantages of the method. We also investigated the PES of Li(8), Al(7)(+), Ag(7), and Ag(2)NH(3) to illustrate potential applications of this new method.     

Bias annealing: a method for obtaining transition paths de novo

Computational studies of dynamics in complex systems require means for generating reactive trajectories with minimum knowledge about the processes of interest. Here, we introduce a method for generating transition paths when an existing one is not already available. Starting from biased paths obtained from steered molecular dynamics, we use a Monte Carlo procedure in the space of whole trajectories to shift gradually to sampling an ensemble of unbiased paths. Application to basin-to-basin hopping in a two-dimensional model system and nucleotide-flipping by a DNA repair protein demonstrates that the method can efficiently yield unbiased reactive trajectories even when the initial steered dynamics differ significantly. The relation of the method to others and the physical basis for its success are discussed.     

On the effect of low concentrations of alcohols on the conformational stability of globular proteins

Low concentrations of alcohols have proven to be able to enlarge the stability curve of globular proteins, by decreasing the cold denaturation temperature and increasing the hot denaturation temperature [S. R. Martin, V. Esposito, P. De Los Rios, A. Pastore and P. A. Temussi, J. Am. Chem. Soc., 2008, 130, 9963-9970]. In order to try to explain these data, I have considered that: (1) an aqueous 2 M MeOH solution can be treated as a uniform liquid, constituted by water molecules, whose density, above the temperature of maximum density, has the same values of neat water, simply shifted by 2 °C toward lower temperatures, whereas, below the temperature of maximum density, it decreases to a slightly lesser extent than the density of neat water; (2) the ΔE(a)(2 M MeOH) quantity, a balance between intra-protein energetic attractions and those with the surrounding solvent molecules, both water and methanol, assumes a constant positive value. These physically-based assumptions, when inserted into the theoretical model developed to rationalize the occurrence of cold denaturation in neat water [G. Graziano, Phys. Chem. Chem. Phys., 2010, 12, 14245-14252], reproduce in a qualitatively correct manner the effect of low concentrations of alcohols.     

Identification of key residues for protein conformational transition using elastic network model

Proteins usually undergo conformational transitions between structurally disparate states to fulfill their functions. The large-scale allosteric conformational transitions are believed to involve some key residues that mediate the conformational movements between different regions of the protein. In the present work, a thermodynamic method based on the elastic network model is proposed to predict the key residues involved in protein conformational transitions. In our method, the key functional sites are identified as the residues whose perturbations largely influence the free energy difference between the protein states before and after transition. Two proteins, nucleotide binding domain of the heat shock protein 70 and human/rat DNA polymerase β, are used as case studies to identify the critical residues responsible for their open-closed conformational transitions. The results show that the functionally important residues mainly locate at the following regions for these two proteins: (1) the bridging point at the interface between the subdomains that control the opening and closure of the binding cleft; (2) the hinge region between different subdomains, which mediates the cooperative motions between the corresponding subdomains; and (3) the substrate binding sites. The similarity in the positions of the key residues for these two proteins may indicate a common mechanism in their conformational transitions.     

Generating arrays with high content and minimal consumption of functional membrane proteins

This paper introduces a widely accessible and straightforward technique for fabricating membrane protein arrays. This technique employs topographically patterned agarose gels to deliver various membrane preparations to glass substrates in a rapid and parallel fashion. It can fabricate more than 30 identical copies of a membrane protein array while requiring only femtomoles of protein. Taking advantage of on-stamp preconcentration, it is able to pattern arrays of multilayered membrane spots with more than 20-fold increased content of membrane proteins compared to existing methods.     

Use of constrained synthetic amino acids in beta-helix proteins for conformational control

A highly constrained amino acid has been introduced in the turn region of a beta-helix to increase the conformational stability of the native fold for nanotechnological purposes. The influence of this specific amino acid replacement in the final organization of beta-helix motifs has been evaluated by combining ab initio first-principles calculations on model systems and molecular dynamics simulations of entire peptide segments. The former methodology, which has been applied to a sequence containing three amino acids, has been used to develop adjusted templates. Calculations indicated that 1-amino-2,2-diphenylcyclopropanecarboxylic acid, a constrained cyclopropane analogue of phenylalanine, exhibits a strong tendency to form and promote folded conformations. On the other hand, molecular dynamics simulations are employed to probe the ability of such a synthetic amino acid to enhance the conformational stability of the beta-helix motif, which is the first requirement for further protein nanoengineering. A highly regular segment from a naturally occurring beta-helix protein was selected as a potential nanoconstruct module. Simulations of wild type and mutated segments revealed that the ability of the phenylalanine analogue to nucleate turn conformations enhances the conformational stability of the beta-helix motif in isolated peptide segments.     

Evolution of physics-based methodology for exploring the conformational energy landscape of proteins

The evolution of our physics-based computational methods for determining protein conformation without the introduction of secondary-structure predictions, homology modeling, threading, or fragment coupling is described. Initial use of a hard-sphere potential captured much of the structural properties of polypeptide chains, and subsequent more refined force fields, together with efficient methods of global optimization provide indications that progress is being made toward an understanding of the interresidue interactions that underlie protein folding.     

Temperature-dependent solid-state electron transport through bacteriorhodopsin: experimental evidence for multiple transport paths through proteins

Electron transport (ETp) across bacteriorhodopsin (bR), a natural proton pump protein, in the solid state (dry) monolayer configuration, was studied as a function of temperature. Transport changes from thermally activated at T > 200 K to temperature independent at <130 K, similar to what we have observed earlier for BSA and apo-azurin. The relatively large activation energy and high temperature stability leads to conditions where bR transports remarkably high current densities above room temperature. Severing the chemical bond between the protein and the retinal polyene only slightly affected the main electron transport via bR. Another thermally activated transport path opens upon retinal oxime production, instead of or in addition to the natural retinal. Transport through either or both of these paths occurs on a background of a general temperature-independent transport. These results lead us to propose a generalized mechanism for ETp across proteins, in which tunneling and hopping coexist and dominate in different temperature regimes.     

Poly-silafluoroalkyleneoligosiloxanes: a class of fluoroelastomers with low glass transition temperature

This work reports some results about the synthesis of unsaturated poly-silafluoroalkyleneoligosiloxanes—derived from TFE telomers—which, after crosslinking, gave elastomeric materials characterized by good flexibility at low temperature, glass transitions below −45 °C and good thermooxidative stability over 250 °C. They are proposed as alternative materials with respect to polyfluoroolefin elastomers.     

Dehydration from conserved stem regions is fundamental for ligand-dependent conformational transition of the adenine-specific riboswitch

Conformational dynamics and observed equilibrium constants for ligand binding of the adenine-specific riboswitch (add-A riboswitch) in the absence of Mg(2+) and presence of various concentrations of poly-ethylene glycol having an average molecular weight of 200 indicated that 54.2 water molecules were released from P2 and P3 stem regions of the add-A riboswitch during conformational transition upon the binding of 2-aminopurine, an analog of the natural ligand adenine.     

Reactions involving transition metals : XIX. Some reactions of perfluoronorbornadiene with low valent transition metal complexes

Perfluoronorbornadiene reacts with the compounds [M(PPh₃)₄] (M = Pt, Pd) and [IrCl(CO)(PMePh₂)₂] to give the adducts [(C₇F₈)M(PPh₃)₂] and [(C₇F₈)IrCl(CO)(PMePh₂)₂] in which one of the double bonds is coordinated to the metal atom. The platinum complex reacts further with [Pt(PPh₃)₄] to give [(C₇F₈){Pt(PPh₃)₂}₂] having both double bonds coordinated to a Pt atom. The carbonylmetal anions [M^?] react to form the mono-substitution products [(C₇F₇)M] (M = Mn(CO)₅, Re(CO)₅, Ir(CO)₂(PPh₃)₂, Rh(CO)₂(PPh₃)₂), but the use of an excess of [Fe(CO)₂(η-C₅H₆)]^? leads to substitution of one fluorine atom on each of the double bonds. The complex having M = Mn(CO)₅ reacts with [Pt(PPh₃)₄] to afford the derivative [(C₇F₇){Mn(CO)₄(PPh₃)}{Pt(PPh₃)₂}], and the compound where M = Ir(CO)₂(PPh₃)₂ undergoes an oxidative addition reaction with acetyl chloride. Oxidative coupling products have been isolated on UV irradiation of a mixture of perfluoronorbornadiene and [Fe(η⁴-CH₂CRCHCH₂)(CO)₃] (R = H, Me), and under similar conditions the reaction with Fe(CO)₅ affords [(C₇F₈)Fe(CO)₄] in very low yield.     

A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins

A three-step approach for multiscale modeling of protein conformational changes is presented that incorporates information about preferred directions of protein motions into a geometric simulation algorithm. The first two steps are based on a rigid cluster normal-mode analysis (RCNMA). Low-frequency normal modes are used in the third step (NMSim) to extend the recently introduced idea of constrained geometric simulations of diffusive motions in proteins by biasing backbone motions of the protein, whereas side-chain motions are biased toward favorable rotamer states. The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation. When applied to a data set of proteins with experimentally observed conformational changes, conformational variabilities are reproduced very well for 4 out of 5 proteins that show domain motions, with correlation coefficients r > 0.70 and as high as r = 0.92 in the case of adenylate kinase. In 7 out of 8 cases, NMSim simulations starting from unbound structures are able to sample conformations that are similar (root-mean-square deviation = 1.0-3.1 ?) to ligand bound conformations. An NMSim generated pathway of conformational change of adenylate kinase correctly describes the sequence of domain closing. The NMSim approach is a computationally efficient alternative to molecular dynamics simulations for conformational sampling of proteins. The generated conformations and pathways of conformational transitions can serve as input to docking approaches or as starting points for more sophisticated sampling techniques.     

Algorithm for rapid calculation of Hessian of conformational energy function of proteins by supercomputer

An improved algorithm is presented for rapid calculation of the hessian matrix for the conformational energy of a protein as a function of only dihedral angles. The speed of the calculation, which is about one order faster than by the previous method, is achieved by two considerations. First, the algorithm is designed to take advantage of the supercomputer pipeline architecture. Second, long-range, nonbonded interactions are cut off and long-range electrostatic interactions are approximated by dipole-dipole interactions in order to reduce the number of pairwise interactions that have to be computed. The results of benchmark tests of the program are given as applied for four globular proteins of different sizes.