Two physics-based models for pH-dependent calculations of protein solubility.

When engineering a protein for its biological function, many physicochemical properties are also optimized throughout the engineering process, and the protein's solubility is among the most important properties to consider. Here, we report two novel computational methods to calculate the pH-dependent protein solubility, and to rank the solubility of mutants. The first is an empirical method developed for fast ranking of the solubility of a large number of mutants of a protein.

A pH-dependent computational approach to the effect of mutations on protein stability.

This article describes a novel software implementation for high-throughput scanning mutagenesis with a focus on protein stability. The approach combines molecular mechanics calculations with calculations of protein ionization and a Gaussian-chain model of electrostatic interactions in unfolded state. Comprehensive testing demonstrates a state-of-the-art accuracy for predicted free energy differences on single, double, and triple mutations with a correlation coefficient R above 0.

pH-selective mutagenesis of protein-protein interfaces: in silico design of therapeutic antibodies with prolonged half-life.

Understanding the effects of mutation on pH-dependent protein binding affinity is important in protein design, especially in the area of protein therapeutics. We propose a novel method for fast in silico mutagenesis of protein-protein complexes to calculate the effect of mutation as a function of pH. The free energy differences between the wild type and mutants are evaluated from a molecular mechanics model, combined with calculations of the equilibria of proton binding.

Observation of enhanced transmission for s-polarized light through a subwavelength slit.

Enhanced optical transmission (EOT) through a single aperture is usually achieved by exciting surface plasmon polaritons with periodic grooves. Surface plasmon polaritons are only excited by p-polarized incident light, i.e.

Fully automated molecular mechanics based induced fit protein-ligand docking method.

We describe a method for docking a ligand into a protein receptor while allowing flexibility of the protein binding site. The method employs a multistep procedure that begins with the generation of protein and ligand conformations. An initial placement of the ligand is then performed by computing binding site hotspots.

A fast and accurate computational approach to protein ionization.

We report a very fast and accurate physics-based method to calculate pH-dependent electrostatic effects in protein molecules and to predict the pK values of individual sites of titration. In addition, a CHARMm-based algorithm is included to construct and refine the spatial coordinates of all hydrogen atoms at a given pH. The present method combines electrostatic energy calculations based on the Generalized Born approximation with an iterative mobile clustering approach to calculate the equilibria of proton binding to multiple titration sites in protein molecules.

LOOPER: a molecular mechanics-based algorithm for protein loop prediction.

We describe a new ab initio method and corresponding program, LOOPER, for the prediction of protein loop conformations. The method is based on a multi-step algorithm (developed as a set of CHARMm scripts) and uses standard CHARMm force field parameters for energy minimization and scoring. One of the main obstacles to ab initio computational loop modeling is the exponential growth of the backbone conformational states with the number of residues in the loop fragment.

The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: a side-chain prediction algorithm based on side-chain backbone interactions.

The basic differences between the 20 natural amino acid residues are due to differences in their side-chain structures. This characteristic design of protein building blocks implies that side-chain-side-chain interactions play an important, even dominant role in 3D-structural realization of amino acid codes. Here we present the results of a comparative analysis of the contributions of side-chain-side-chain (s-s) and side-chain-backbone (s-b) interactions to the stabilization of folded protein structures within the framework of the CHARMm molecular data model.

A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction.

A range of methods has been developed to predict transmembrane helices and their topologies. Although most of these algorithms give good predictions, no single method consistently outperforms the others. However, combining different algorithms is one approach that can potentially improve the accuracy of the prediction.

Influence of tacrine on dopamine-induced reactions of the gastric smooth muscle of rats.

The clinical usage of the cholinesterase inhibitor tacrine for treatment of Alzheimer's disease is accompanied by adverse effects on the gastrointestinal tract. These adverse effects are a result of the direct action of tacrine on the intestinal smooth muscles or of the modulation of certain neurotransmitters regulating gastrointestinal functions. Dopamine is a neurotransmitter that modulates gastrointestinal motility.

Effects of GABA(B) receptor antagonists on spontaneous and on GABA-induced mechanical activity of guinea-pig smooth muscle preparations.

The majority of GABA(B) receptor antagonists have been based on alterations of the acidic moiety of gamma-aminobutyric acid (GABA) or baclofen, such as the first selective antagonist phaclofen. More recently, a new structural class of compounds derived by p-alkyl substitution in the phosphinic analog of GABA, such as CGP35348 (3-amino-propyl-(diethoxymethyl)-phosphinic acid), have been introduced as GABA(B) receptor antagonists. The present study examine the influence of a series of structurally related phosphinic acid analogues on mechanical activity and their effect on GABA-induced reactions in ileal smooth muscle.

pK(a) Calculations suggest storage of an excess proton in a hydrogen-bonded water network in bacteriorhodopsin.

Calculations of protonation states and pK(a) values for the ionizable groups in the resting state of bacteriorhodopsin have been carried out using the recently available 1.55 A resolution X-ray crystallographic structure. The calculations are in reasonable agreement with the available experimental data for groups on or near the ion transport chain (the retinal Schiff base; Asp85, 96, 115, 212, and Arg82).

Electrostatic coupling to pH-titrating sites as a source of cooperativity in protein-ligand binding.

This paper describes an alternative mechanism for the cooperative binding of charged ligands to proteins. The ligand-binding sites are electrostatically coupled to protein side chains that can undergo protonation and deprotonation. The binding of one ligand alters the protein's protonation equilibrium in a manner that makes the the binding of the second ligand more favorable.

A seven-years experience in treatment of childhood ALL in Bulgaria.

After analyzing nonsatisfactory therapeutic results in the 1970s and early 1980s, the 81-01 treatment protocol of the Dana-Farber Cancer Institute was initiated in 1987 in the Children's Oncohaematology Clinic in Sofia, Bulgaria. Two hundred thirty patients were enrolled with a period of observation of a minimum of 14 and a maximum of 97 months; the median age was 5.83 +/- 3.

Optimization of the electrostatic interactions between ionized groups and peptide dipoles in proteins.

The three-dimensional optimization of the electrostatic interactions between the charged amino acid residues and the peptide partial charges was studied by Monte-Carlo simulations on a set of 127 nonhomologous protein structures with known atomic coordinates. It was shown that this type of interaction is very well optimized for all proteins in the data set, which suggests that they are a valuable driving force, at least for the native side-chain conformations. Similar to the optimization of the charge-charge interactions (Spassov VZ, Karshikoff AD, Ladenstein R, 1995, Protein Sci 4:1516-1527), the optimization effect was found more pronounced for enzymes than for proteins without enzymatic function.

Computer simulation of excitation-contraction coupling in cardiac muscle. A study of the regulatory role of calcium binding to troponin C.

The influence of a change of troponin concentration as well of a change of binding and dissociation of Ca2+ ions to the regulatory protein troponin C on the time course of isometric tension has been studied, using a mathematical model developed to investigate excitation-contraction coupling in cardiac muscle cells. The numerical simulations show that peak amplitude, rate of force development, time to peak tension and relaxation time depend significantly on the above parameters even in the case when the equilibrium dissociation constant remains unchanged. The obtained results might be useful for the planing of new experiments in the view of the fact that no similar data have been reported for cardiac muscle cells as yet.

Effects of GABAB receptor antagonists on learning and memory retention in a rat model of absence epilepsy.

A variety of animal models of absence epilepsy have been described and among these exists a genetically susceptible strain of rat (genetic absence epilepsy rats of Strasbourg (GAERS)). These rats produce periods of behavioural arrest with simultaneous production of cortical spike and wave discharges (SWD). GABAB receptor antagonists suppress completely the production of these spike and wave discharges.

Relationship between accessibility and reactivity of Lys, Met and Tyr in subtilisins DY and Carlsberg.

The chemical reactivities of lysyl, tyrosyl and methionyl residues in subtilisin DY are compared with the computed accessibilities to the water molecules of the corresponding sensitive atoms in the crystal structure of subtilisin Carlsberg. A good correlation between accessibilities and reactivity was established for the nonionized specific reagents glyceraldehyde and chloramine T used for modification of lysine and methionine residues, respectively. In a few cases an apparent deviation from the general relationship was established.

The optimization of protein-solvent interactions: thermostability and the role of hydrophobic and electrostatic interactions.

Protein-solvent interactions were analyzed using an optimization parameter based on the ratio of the solvent-accessible area in the native and the unfolded protein structure. The calculations were performed for a set of 183 nonhomologous proteins with known three-dimensional structure available in the Protein Data Bank. The dependence of the total solvent-accessible surface area on the protein molecular mass was analyzed.

Optimization of the electrostatic interactions in proteins of different functional and folding type.

The 3-dimensional optimization of the electrostatic interactions between the charged amino acid residues was studied by Monte Carlo simulations on an extended representative set of 141 protein structures with known atomic coordinates. The proteins were classified by different functional and structural criteria, and the optimization of the electrostatic interactions was analyzed. The optimization parameters were obtained by comparison of the contribution of charge-charge interactions to the free energy of the native protein structures and for a large number of randomly distributed charge constellations obtained by the Monte Carlo technique.

Electrostatic properties of two porin channels from Escherichia coli.

The electrostatic interactions in the channels of OmpF and PhoE porins from Escherichia coli were analysed on the basis of a macroscopic multi-dielectric model of the protein-membrane complex derived from the respective porin X-ray structures. The membrane was represented as layers of distinct dielectric constants corresponding to the aliphatic core and the polar head groups of the lipids. The pKa values of the titratable groups and the electrostatic field in the region of the channel were calculated by the finite difference technique.

Structural modeling and electrostatic properties of aspartate transcarbamylase from Saccharomyces cerevisiae.

In Saccharomyces cerevisiae the first two reactions of the pyrimidine pathway are catalyzed by a multifunctional protein which possesses carbamylphosphate synthetase and aspartate transcarbamylase activities. Genetic and proteolysis studies suggested that the ATCase activity is carried out by an independently folded domain. In order to provide structural information for ongoing mutagenesis studies, a model of the three-dimensional structure of this domain was generated on the basis of the known X-ray structure of the related catalytic subunit from E.

Spatial optimization of electrostatic interactions between the ionized groups in globular proteins.

A model approach is suggested to estimate the degree of spatial optimization of the electrostatic interactions in protein molecules. The method is tested on a set of 44 globular proteins, representative of the available crystallographic data. The theoretical model is based on macroscopic computation of the contribution of charge-charge interactions to the electrostatic term of the free energy for the native proteins and for a big number of virtual structures with randomly distributed on protein surface charge constellations (generated by a Monte-Carlo technique).

Urea unfolding and stability of gamma-II crystallin.

The conformational stability of gamma-II crystallin at pH 7.0 was estimated by studying its urea denaturation at isothermal conditions. The conformational states were monitored by far UV-CD and fluorescence measurements.

Effect of insulin and glucagon on the mobility of ESR-probes incorporated in rat liver plasma membranes.

1. The effect of different concentrations of insulin (INS) and glucagon (GLU) on the rotational mobility of a membrane-incorporated spin probe 2,2-6,6-tetramethyl-4-capriloyl piperidine-1-oxil (C7) was investigated by electron spin resonance (ESR) technique. 2.