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.     

Fiber-assisted detection with photon number resolution

We report the development of a photon-number-resolving detector based on a fiber-optical setup and a pair of standard avalanche photodiodes. The detector is capable of resolving individual photon numbers and operates on the well-known principle by which a single-mode input state is split into a large number (eight) of output modes. We reconstruct the photon statistics of weak coherent input light from experimental data and show that there is a high probability of inferring the input photon number from a measurement of the number of detection events on a single run.     

Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods

A united-residue model of polypeptide chains developed in our laboratories with united side-chains and united peptide groups as interaction sites is presented. The model is designed to work in continuous space; hence efficient global-optimization methods can be applied. In this work, we adopted the distance-scaling method that is based on continuous deformation of the original rugged energy hypersurface to obtain a smoothed surface. The method has been applied successfully to predict the structures of simple motifs, such as the three-helix bundle structure of the 10-58 fragment of staphylococcal protein A in de novo folding simulations and more complicated motifs in inverse-folding simulations. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Endpoints of set-valued dynamical systems of asymptotic contractions of Meir–Keeler type and strict contractions in uniform spaces

In this paper, we introduce the concepts of the set-valued dynamical systems of asymptotic contractions of Meir–Keeler type and set-valued dynamical systems of strict contractions in uniform spaces and we present a method which is useful for establishing conditions guaranteeing the existence and uniqueness of endpoints of these contractions and the convergence to these endpoints of all generalized sequences of iterations of these contractions. The result, concerning the investigations of problems of the set-valued asymptotic fixed point theory, include some well-known results of Meir and Keeler, Kirk and Suzuki concerning the asymptotic fixed point theory of single-valued maps in metric spaces. The result, concerning set-valued strict contractions (in which the contractive coefficient is not constant), is different from the result of Yuan concerning the existence of endpoints of Tarafdar–Vyborny generalized contractions (in which the contractive coefficient is constant) in bounded metric spaces and provides some examples of Tarafdar–Yuan topological contractions in compact uniform spaces. Definitions and results presented here are new for set-valued dynamical systems in uniform, locally convex and metric spaces and even for single-valued maps. Examples show a fundamental difference between our results and the well-known ones.     

New catalytic route to functionalized vinylboronates

Vinylsubstituted boronates i.e. vinyldioxaborolane and vinyldioxaborinane react regioselectively with olefins in the presence of RuHCl(CO)(PCy3)2 with the formation of functionalized vinylboron derivatives. The reaction opens a new catalytic route for preparation of organoboranes.     

On iterative convexity of diffeomorphism

Abstract

A function f is said to be iteratively convex if f possesses convex iterative roots of all orders. We give several constructions of iteratively convex diffeomorphisms and explain the phenomenon that the non-existence of convex iterative roots is a typical property of convex functions. We show also that a slight perturbation of iteratively convex functions causes loss of iterative convexity. However, every convex function can be approximate by iteratively convex functions.     

Modified cyclodextrin polymers as selective ion carriers for Pb(II) separation across plasticized membranes

In the present work the hydrophobic β-cyclodextrin (β-CD) polymers have been used as macrocyclic ion carriers for separation of Pb(II), Zn(II), and Cu(II) ions from dilute aqueous solutions by transport across polymer inclusion membranes. The β-CD polymers were prepared by cross-linking of β-CD with 2-(1-docosenyl)-succinic anhydride derivatives in anhydrous N,N-dimethylformamide in the presence of NaH. The metal ions were transported from aqueous solutions containing heavy metal ions through plasticizer triacetate membranes with dimer and polymer β-CD derivatives into distilled water. The selectivity of lead(II) over other metal ions in the transport through polymer inclusion membrane was very high, especially for dimer cyclodextrin carrier. In the case of competitive transport of Pb(II), Cu(II), and Zn(II) ions through plasticized immobilized membranes the selectivity of process is controlled via formation of ion pairs of β-CD hydroxyl groups with metal cations. The polymer and dimer of β-CD linked by 2-(1-docosenyl)-derivative used as ionic carriers for competitive transport of metal ions show preferential selectivity order: Pb(II)  Cu(II) > Zn(II). Application of ion carriers mixtures (β-CD polymers and palmitic acid) causes the increase of Pb(II) maximal removal from dilute aqueous solution. The weight-average molecular weight (M_W) and the chemical structure of the β-CD polymers were determined using high-performance size exclusion chromatography with refractive index detector, and ¹H NMR spectroscopy.     

Implementations of Nosé-Hoover and Nosé-Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain

Molecular dynamics (MD) simulations generate a canonical ensemble only when integration of the equations of motion is coupled to a thermostat. Three extended phase space thermostats, one version of Nose-Hoover and two versions of Nose-Poincare, are compared with each other and with the Berendsen thermostat and Langevin stochastic dynamics. Implementation of extended phase space thermostats was first tested on a model Lennard-Jones fluid system; subsequently, they were implemented with our physics-based protein united-residue (UNRES) force field MD. The thermostats were also implemented and tested for the multiple-time-step reversible reference system propagator (RESPA). The velocity and temperature distributions were analyzed to confirm that the proper canonical distribution is generated by each simulation. The value of the artificial mass constant, Q, of the thermostat has a large influence on the distribution of the temperatures sampled during UNRES simulations (the velocity distributions were affected only slightly). The numerical stabilities of all three algorithms were compared with each other and with that of microcanonical MD. Both Nose-Poincare thermostats, which are symplectic, were not very stable for both the Lennard-Jones fluid and UNRES MD simulations started from nonequilibrated structures which implies major changes of the potential energy throughout a trajectory. Even though the Nose-Hoover thermostat does not have a canonical symplectic structure, it is the most stable algorithm for UNRES MD simulations. For UNRES with RESPA, the "extended system inside-reference system propagator algorithm" of the RESPA implementation of the Nose-Hoover thermostat was the only stable algorithm, and enabled us to increase the integration time step.     

Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins

We report the modification and parametrization of the united-residue (UNRES) force field for energy-based protein structure prediction and protein folding simulations. We tested the approach on three training proteins separately: 1E0L (beta), 1GAB (alpha), and 1E0G (alpha + beta). Heretofore, the UNRES force field had been designed and parametrized to locate native-like structures of proteins as global minima of their effective potential energy surfaces, which largely neglected the conformational entropy because decoys composed of only lowest-energy conformations were used to optimize the force field. Recently, we developed a mesoscopic dynamics procedure for UNRES and applied it with success to simulate protein folding pathways. However, the force field turned out to be largely biased toward -helical structures in canonical simulations because the conformational entropy had been neglected in the parametrization. We applied the hierarchical optimization method, developed in our earlier work, to optimize the force field; in this method, the conformational space of a training protein is divided into levels, each corresponding to a certain degree of native-likeness. The levels are ordered according to increasing native-likeness; level 0 corresponds to structures with no native-like elements, and the highest level corresponds to the fully native-like structures. The aim of optimization is to achieve the order of the free energies of levels, decreasing as their native-likeness increases. The procedure is iterative, and decoys of the training protein(s) generated with the energy function parameters of the preceding iteration are used to optimize the force field in a current iteration. We applied the multiplexing replica-exchange molecular dynamics (MREMD) method, recently implemented in UNRES, to generate decoys; with this modification, conformational entropy is taken into account. Moreover, we optimized the free-energy gaps between levels at temperatures corresponding to a predominance of folded or unfolded structures, as well as to structures at the putative folding-transition temperature, changing the sign of the gaps at the transition temperature. This enabled us to obtain force fields characterized by a single peak in the heat capacity at the transition temperature. Furthermore, we introduced temperature dependence to the UNRES force field; this is consistent with the fact that it is a free-energy and not a potential energy function. beta