Structure of folding intermediates at pH 4.0 and native state of microbial transglutaminase

Recombinant microbial transglutaminase has been expressed in Escherichia coli as insoluble inclusion bodies. After we searched for refolding conditions, refolding of the protein could be done by first dilution of the unfolded enzyme in a buffer at pH 4.0, and then by titration of the pH from 4.0 to 6.0. CD analysis showed that a burst of secondary structure formation occurred within the dead time of the experiment and accounted for 75% of the signal change in the far UV CD, with little tertiary structure being formed. This burst was followed by slow rearrangement of the secondary structure accompanied by formation of tertiary structure. The secondary and tertiary structures of the final sample at pH 4.0, corresponding to the folding intermediate, were different from these structures at pH 6.0. Once the native structure was obtained, acidification of the native protein to pH 4.0 did not lead to a structure like that of the folding intermediate. Sedimentation velocity analysis showed that the folding intermediate had an expanded structure and contained no other structure species including large aggregates.     

Antibodies against the chemically synthesized genome-linked protein of poliovirus react with native virus-specific proteins

The genome-linked protein (VPg) of poliovirus has been chemically synthesized, coupled to bovine serum albumin carrier and injected into rabbits. An antibody response was elicited not only by the full-length synthetic VPg peptide, but also by a synthetic 14-amino acid carboxy-terminal peptide. All antisera reacted with virus-specific proteins from HeLa cells infected with poliovirus. Three of these proteins have previously been implicated by others as precursors of VPg. No free cytoplasmic VPg could be detected, and the antibodies did not react with radiolabeled proteins from uninfected cells.     

The acid-induced folded state of Sac7d is the native state

Sac7d unfolds at low pH in the absence of salt, with the greatest extent of unfolding obtained at pH 2. We have previously shown that the acid unfolded protein is induced to refold by decreasing the pH to 0 or by addition of salt (McCrary BS, Bedell J. Edmondson SP, Shriver JW, 1998, J Mol Biol 276:203-224). Both near-ultraviolet circular dichroism spectra and ANS fluorescence enhancements indicate that the acid- and salt-induced folded states have a native fold and are not molten globular. 1H,15N heteronuclear single quantum coherence NMR spectra confirm that the native, acid-, and salt-induced folded states are essentially identical. The most significant differences in amide 1H and 15N chemical shifts are attributed to hydrogen bonding to titrating carboxyl side chains and through-bond inductive effects. The 1H NMR chemical shifts of protons affected by ring currents in the hydrophobic core of the acid- and salt-induced folded states are identical to those observed in the native. The radius of gyration of the acid-induced folded state at pH 0 is shown to be identical to that of the native state at pH 7 by small angle X-ray scattering. We conclude that acid-induced collapse of Sac7d does not lead to a molten globule but proceeds directly to the native state. The folding of Sac7d as a function of pH and anion concentration is summarized with a phase diagram that is similar to those observed for other proteins that undergo acid-induced folding except that the A-state is encompassed by the native state. These results demonstrate that formation of a molten globule is not a general property of proteins that are refolded by acid.     

Characterization of the backbone geometry of protein native state structures

We present a simple method for analyzing the geometry of noncovalent residue-residue interactions stabilizing the protein structure, which takes into account the constraints on the local backbone geometry. We find that the principal geometrical constraints are amino acid aspecific and are associated with hydrogen bond formation in helices and sheets. In contrast, amino acid residues in nonhelical and nonextended conformations, which make noncovalent interactions stabilizing the protein tertiary structure, display greater flexibility. We apply the method to an analysis of the packing of helices in helical bundle proteins requiring an efficient packing of amino acid side-chains of the interacting helices.     

Revealing the nature of the native state ensemble through cold denaturation

Recent advances in NMR methodology have enabled the structural analysis of proteins at temperatures far below the freezing point of water, thus opening a window to the cold denaturation process. Although the phenomenon of cold denaturation has been known since the mid-1970s, the freezing point of water has prevented detailed and structurally resolved studies without application of additional significant perturbations of the protein ensemble. As a result, the cold-denatured state and the process of cold denaturation have gone largely unstudied. Here, the structural and thermodynamic basis of cold denaturation is explored with emphasis placed on the insights that are uniquely ascertained from low-temperature studies. It is shown that the noncooperative cold-induced unfolding of protein results in the population of partially folded states that cannot be accessed by other techniques. The structurally resolved view of the cold denaturation process therefore can provide direct access to the cooperative substructures within the protein molecule and provide an unprecedented structurally resolved picture of the states that comprise the native state ensemble.     

Development of a semi-closed underwater breathing apparatus, the "eOBA"

Nippon Sanso K.K developed a compact semi-closed underwater breathing apparatus, the eOBA. It consists of a mouthpiece, manifold with a purge valve, two spring-loaded flexible tubes, a small CO2 absorbent canister (net wt. = 190g), and two compact high pressure bottles (50ccx2: 190kg/cm2: 80%O2, 20%N2) with a regulator which supplies the gas at the constant flow rate of 1.5 l/min and lasts for 10 min. Thus, a counterlung is not incorporated. However, spring-loaded tubes act as a counterlung since its volume increases to 3.5 l when fully inflated. Dives to a depth of 5m are also recommended because of no bypass valve. This new eOBA was tested using the mechanical breathing machine and CO2 supply system to the circuit. For the various combinations of tidal volumes (0.5-2.5 l) and respiratory rates (10-20 breaths/min), the pressure at the mouthpiece, respiratory volume and the CO2 level were continuously monitored. The CO2 absorption rates were then calculated. The thin sloping P-V loops demonstrate that the eOBA is a flow dependent type of apparatus. It was found that the external work of breathing (0.1 kg.m/l at 30 l/min) were allowable. The CO2 absorption rates were sufficient when minute ventilation increased to 30 l/min. Thus, results show that the eOBA must be suitable for shallow and short dives.     

Evaluation of a semi-closed underwater breathing apparatus, the "eOBA"

Semi-closed underwater breathing apparatus has commonly been used among military and commercial divers, but never available for recreational divers because of complicated operations, difficulties of maintenance, and expensiveness. Nippon Sanso K.K. has newly deployed a semi-closed circuit underwater breathing apparatus called the "eOBA". It is especially designed for divers to enjoy shallow (max. 5 m) and short (10 min.) dives. This eOBA was evaluated from manned testing based on physiological requirements for the apparatus. Four male and four female subjects participated in the three test trials. Subjects maintained their position at the depths of 2 m and 4 m for 10 min. and e exercised on the underwater ergometer at the depth of 2.4 m. The pressure at the mouthpiece, tidal volume, breathing rate, the inspired O2 level, CO2 level were monitored on breath-by-breath basis. The inspired O2 level ranged from 45% (at exercise) to 60% (at rest) and the inspired CO2 level were kept less than 1.0% in the most cases. The P-V loop indicated relatively little external work of breathing (less than 0.1 kg.m/l) and allowable peak pressures (less than 25cmH2O). Results show that the eOBA meets the standards sufficiently under the test conditions and is a safe apparatus for recreational divers if it is properly used.     

Optimizing protein folding to the native state in bacteria.

A correctly folded protein is usually both active and soluble. This review focuses on novel ways to improve the folding of recombinant proteins during production in bacteria and includes a few tips for refolding proteins. Major results in correlating protein primary structure with proper folding and stability, and the production of viral antigens and antibodies in bacteria are also discussed.     

Assessing the native state conformational distribution of ubiquitin by peptide acidity

At equilibrium, every energetically feasible conformation of a protein occurs with a non-zero probability. Quantitative analysis of protein flexibility is thus synonymous with determining the proper Boltzmann-weighting of this conformational distribution. The exchange reactivity of solvent-exposed amide hydrogens greatly varies with conformation, while the short-lived peptide anion intermediate implies an insensitivity to the dynamics of conformational motion. Amides that are well-exposed in model conformational ensembles of ubiquitin vary a million-fold in exchange rates which continuum dielectric methods can predict with an rmsd of 3. However, the exchange rates for many of the more rarely exposed amides are markedly overestimated in the PDB-deposited 2K39 and 2KN5 ubiquitin ensembles, while the 2NR2 ensemble predictions are largely consistent with those of the Boltzmann-weighted conformational distribution sampled at the level of 1%. The correlation between the fraction of solvent-accessible conformations for a given amide hydrogen and the exchange rate constant for that residue provides a useful monitor of the degree of completeness with which a given ensemble has sampled the energetically accessible conformational space. These exchange predictions correlate with the degree to which each ensemble deviates from a set of 46 ubiquitin X-ray structures. Kolmogorov-Smirnov analysis for the distribution of intra- and inter-ensemble pairwise structural rmsd values assisted the identification of a subensemble of 2K39 that eliminates the overestimations of hydrogen exchange rates observed for the full ensemble. The relative merits of incorporating experimental restraints into the conformational sampling process are compared to using these restraints as filters to select subpopulations consistent with the experimental data.