Rubredoxin Variant Folds without Iron

Pyroccocus furiosus rubredoxin (PFRD), like most studied hyperthermophilic proteins, does not undergo reversible folding. The irreversibility of folding is thought to involve PFRD’s iron-binding site. Here we report a PFRD variant (PFRD-XC4) whose iron binding site was redesigned to eliminate iron binding using a computational design algorithm. PFRD-XC4 folds without iron and exhibits reversible folding with a melting temperature of 82 °C, a thermodynamic stability of 3.2 kcal mol^(-1) at 1 °C, and NMR chemical shifts similar to that of the wild-type protein. This variant should provide a tractable model system for studying the thermodynamic origins of protein hyperthermostability

Evaluating and optimizing computational protein design force fields using fixed composition-based negative design

An accurate force field is essential to computational protein design and protein fold prediction studies. Proper force field tuning is problematic, however, due in part to the incomplete modeling of the unfolded state. Here, we evaluate and optimize a protein design force field by constraining the amino acid composition of the designed sequences to that of a well behaved model protein. According to the random energy model, unfolded state energies are dependent only on amino acid composition and not the specific arrangement of amino acids. Therefore, energy discrepancies between computational predictions and experimental results, for sequences of identical composition, can be directly attributed to flaws in the force field's ability to properly account for folded state sequence energies. This aspect of fixed composition design allows for force field optimization by focusing solely on the interactions in the folded state. Several rounds of fixed composition optimization of the 56-residue β1 domain of protein G yielded force field parameters with significantly greater predictive power: Optimized sequences exhibited higher wild-type sequence identity in critical regions of the structure, and the wild-type sequence showed an improved Z-score. Experimental studies revealed a designed 24-fold mutant to be stably folded with a melting temperature similar to that of the wild-type protein. Sequence designs using engrailed homeodomain as a scaffold produced similar results, suggesting the tuned force field parameters were not specific to protein G

Polar residues in the protein core of Escherichia coli thioredoxin are important for fold specificity

Most globular proteins contain a core of hydrophobic residues that are inaccessible to solvent in the folded state. In general, polar residues in the core are thermodynamically unfavorable except when they are able to form intramolecular hydrogen bonds. Compared to hydrophobic interactions, polar interactions are more directional in character and may aid in fold specificity. In a survey of 263 globular protein structures, we found a strong positive correlation between the number of polar residues at core positions and protein size. To probe the importance of buried polar residues, we experimentally tested the effects of hydrophobic mutations at the five polar core residues in Escherichia coli thioredoxin. Proteins with single hydrophobic mutations (D26I, C32A, C35A, T66L, and T77V) all have cooperative unfolding transitions like the wild type (wt), as determined by chemical denaturation. Relative to wt, D26I is more stable while the other point mutants are less stable. The combined 5-fold mutant protein (IAALV) is less stable than wt and has an unfolding transition that is substantially less cooperative than that of wt. NMR spectra as well as amide deuterium exchange indicate that IAALV is likely sampling a number of low-energy structures in the folded state, suggesting that polar residues in the core are important for specifying a well-folded native structure

Housing and labor market distortions in Poland : linkages and policy implications

Poland's housing and macroeconomic policies have restricted investments in housing and urban infrastructure to a level well below that of other European countries. This has resulted in a shortage of housing typified by 15 to 20 year waits for government sponsored housing. Shortages of this magnitude are likely to cause distortions with impacts on patterns of savings and consumption, the price level, and on the functioning of labor markets. This paper focuses particularly on how housing market distortions are transmitted to labor markets, with impacts on rates of migration, relative wage levels among different regions, and, by implication, on the productivity of the Polish work force. The basic thesis of the paper is that if housing markets are prevented from reaching their competitive equilibrium that labor markets will similarly be prevented. Evidence is examined on the extent of housing and labor market disequilibria, and estimates econometric models that relate internal migration and relative wages to alternative measures of housing market disequilibria. From these analyses it is concluded that labor markets are in fact distorted by housing market distortions, with potentially major macroeconomic costs.Banks&Banking Reform,Municipal Financial Management,Housing&Human Habitats,Public Sector Economics&Finance,Urban Housing

Change Blindness in the Synthetic Vision Primary Flight Display: Comparing Eye Tracking Patterns with Pilot Attention

There have been a number of important advances in aviation technology that have made the safety rating of flying the best that it has ever been. One of the most important advances made has been in the interface that the pilot relies on for their most critical information during flight. New aviation displays have empirically shown a wide range of improvements across pilot performance. Despite these improvements, there is still a high possibility that pilots may miss pertinent information that changes may occur simultaneously with some sort of distraction - a concept known as change blindness. This study analyzed how pilots use their primary flight display during a change blindness paradigm in conjunction with an eye tracker to investigate the link between where the pilot was visually looking and the instruments they were attending. Patterns indicated that pilots use a hub-and-spoke eye scanning pattern during normal flight, focusing mostly in the center of the display. Despite this, change blindness had little effect, emphasizing the display\u27s inherent ease of use

Phenalene-phosphazene complexes: effect of exocyclic charge densities on the cyclotriphosphazene ring system

The synthesis and properties of a new series of 1,9-diamino-substituted phenalene complexes of the cyclotriphosphazene ring system is described. One of the compounds is shown to be amphoteric, and this behavior allows an examination of the response of the phosphazene linkage to variations in exocyclic charge density at the spiro center in a plane perpendicular to the cyclotriphosphazene ring system. ^(31)P NMR spectroscopy indicates that substituent lone pairs with this orientation are not effective in long-range delocalization within the phosphazene linkage (in accord with our theoretical model of spiro delocalization). An X-ray crystal structure of one compound (7) identifies the presence of clathrated molecules of chloroform together with doubly hydrogen-bonded pairs of the phenalene-phosphazene complexes in the lattice. Crystal data for 7 (C_(13)H_8Cl_4N_5P_3•CHCl_3): monoclinic space group P2_1/c, a = 12.401 (4) Å, b = 28.404 (6) Å, c = 12.962 (3) Å, β = 91.76 (2)°, V = 4564 (2) Å^3, Z = 8, R = 0.050 for 4525 reflections

DREIDING: A generic force field for molecular simulations

We report the parameters for a new generic force field, DREIDING, that we find useful for predicting structures and dynamics of organic, biological, and main-group inorganic molecules. The philosophy in DREIDING is to use general force constants and geometry parameters based on simple hybridization considerations rather than individual force constants and geometric parameters that depend on the particular combination of atoms involved in the bond, angle, or torsion terms. Thus all bond distances are derived from atomic radii, and there is only one force constant each for bonds, angles, and inversions and only six different values for torsional barriers. Parameters are defined for all possible combinations of atoms and new atoms can be added to the force field rather simply. This paper reports the parameters for the "nonmetallic" main-group elements (B, C, N, 0, F columns for the C, Si, Ge, and Sn rows) plus H and a few metals (Na, Ca, Zn, Fe). The accuracy of the DREIDING force field is tested by comparing with (i) 76 accurately determined crystal structures of organic compounds involving H, C, N, 0, F, P, S, CI, and Br, (ii) rotational barriers of a number of molecules, and (iii) relative conformational energies and barriers of a number of molecules. We find excellent results for these systems

Exhaustive mutagenesis of six secondary active-site residues in Escherichia coli chorismate mutase shows the importance of hydrophobic side chains and a helix N-capping position for stability and catalysis

Secondary active-site residues in enzymes, including hydrophobic amino acids, may contribute to catalysis through critical interactions that position the reacting molecule, organize hydrogen-bonding residues, and define the electrostatic environment of the active site. To ascertain the tolerance of an important model enzyme to mutation of active-site residues that do not directly hydrogen bond with the reacting molecule, all 19 possible amino acid substitutions were investigated in six positions of the engineered chorismate mutase domain of the Escherichia coli chorismate mutase-prephenate dehydratase. The six secondary active-site residues were selected to clarify results of a previous test of computational enzyme design procedures. Five of the positions encode hydrophobic side chains in the wild-type enzyme, and one forms a helix N-capping interaction as well as a salt bridge with a catalytically essential residue. Each mutant was evaluated for its ability to complement an auxotrophic chorismate mutase deletion strain. Kinetic parameters and thermal stabilities were measured for variants with in vivo activity. Altogether, we find that the enzyme tolerated 34% of the 114 possible substitutions, with a few mutations leading to increases in the catalytic efficiency of the enzyme. The results show the importance of secondary amino acid residues in determining enzymatic activity, and they point to strengths and weaknesses in current computational enzyme design procedures