Factors correlating with significant differences between X-ray structures of myoglobin.

S-nitrosylation is a post-translational protein modification that can alter the function of a variety of proteins. Despite the growing wealth of information that this modification may have important functional consequences, little is known about the structure of the moiety or its effect on protein tertiary structure. Here we report high-resolution x-ray crystal structures of S-nitrosylated and unmodified blackfin tuna myoglobin, which demonstrate that in vitro S-nitrosylation of this protein at the surface-exposed Cys-10 directly causes a reversible conformational change by "wedging" apart a helix and loop. Furthermore, we have demonstrated in solution and in a single crystal that reduction of the S-nitrosylated myoglobin with dithionite results in NO cleavage from the sulfur of Cys-10 and rebinding to the reduced heme iron, showing the reversibility of both the modification and the conformational changes. Finally, we report the 0.95-A structure of ferrous nitrosyl myoglobin, which provides an accurate structural view of the NO coordination geometry in the context of a globin heme pocket.

Tear lipocalin (TL), a major protein of human tears, binds a broad array of endogenous ligands. pH-dependent ligand binding in TL may have functional implications in tears. Previously, conformational selections of the AB and GH loops have been implicated in ligand binding by site-directed tryptophan fluorescence (SDTF). In this study, SDTF was applied to the AB and GH loops to investigate pH-driven conformational changes relevant to ligand binding. Both loops demonstrate significant but distinct conformational rearrangements over a wide pH range. In the low-pH transition, from 7.3 to 3.0, residues of the GH loop exhibit decreased solvent accessibilities. In acrylamide quenching experiments, the average quenching rate constant (k(q), accessibility parameter) of the residues in the GH loop is decreased approximately 38%, from 2.1 x 10(9) to 1.3 x 10(9) M(-1) s(-1). However, despite the significant changes in accessibilities for some residues in the AB loop, the average accessibility per residue remained unchanged (average k(q) = 1.2 M(-1) s(-1)). Accordingly, the low-pH transition induces conformational changes that reshuffle the accessibility profiles of the residues in the AB loop. A significant difference in the titration curves between the holo and apo forms of the W28 mutant suggests that the protonation states of the residues around position 28 modulate conformational switches of the AB loop relevant to ligand binding.

Proton magnetic resonance study of the histidine residues of sperm whale and horse myoglobins

We developed a new computational algorithm for the accurate identification of ligand binding envelopes rather than surface binding sites. We performed a large scale classification of the identified envelopes according to their shape and physicochemical properties. The predicting algorithm, called PocketFinder, uses a transformation of the Lennard-Jones potential calculated from a three-dimensional protein structure and does not require any knowledge about a potential ligand molecule. We validated this algorithm using two systematically collected data sets of ligand binding pockets from complexed (bound) and uncomplexed (apo) structures from the Protein Data Bank, 5616 and 11,510, respectively. As many as 96.8% of experimental binding sites were predicted at better than 50% overlap level. Furthermore 95.0% of the asserted sites from the apo receptors were predicted at the same level. We demonstrate that conformational differences between the apo and bound pockets do not dramatically affect the prediction results. The algorithm can be used to predict ligand binding pockets of uncharacterized protein structures, suggest new allosteric pockets, evaluate feasibility of protein-protein interaction inhibition, and prioritize molecular targets. Finally the data base of the known and predicted binding pockets for the human proteome structures, the human pocketome, was collected and classified. The pocketome can be used for rapid evaluation of possible binding partners of a given chemical compound.

On the difference in stability between horse and sperm whale myoglobins

Needs for and Barriers to Correctional Mental Health Services: Inmate Perceptions

Author response: Limitations of principal components in quantitative genetic association models for human studies

Decision letter: Limitations of principal components in quantitative genetic association models for human studies

Editor's evaluation: Limitations of principal components in quantitative genetic association models for human studies

A Fourier transform infrared spectroscopic (FTIR) study of porcine and bovine pancreatic phospholipase A 2 and their interaction with substrate analogues and a transition-state inhibitor

We find that a single region on the surface of different species of myoglobin appears to be immunodominant for T lymphocytes, even though the residues in that region vary sufficiently that the T cells immune to one myoglobin do not crossreact with other myoglobins bearing substitutions at that site. Immunization of B10.S mice with sperm whale myoglobin elicits T-lymphocyte populations capable of recognizing sperm whale myoglobin but not horse myoglobin, whereas the converse is true when these mice are immunized with horse myoglobin. Using a series of myoglobin variants, we tested the effect of changes in primary sequence on the T-lymphocyte proliferative response. We were able to divide the myoglobin variants into two groups, depending on whether they cross stimulate sperm whale immune or horse immune T lymphocytes. The patterns of cross stimulation of both populations of myoglobin immune T lymphocytes were explained by amino acid substitutions at position 109. However, because sperm whale and horse myoglobin differ at this residue (glutamate vs. aspartate, respectively), T lymphocytes immune to each myoglobin do not crossreact with the other myoglobin. Additional data suggest that this immunodominant epitope also includes other residues nearby on the surface of the native molecule. Mixing experiments showed that the specificity was that of T lymphocytes and not antigen-presenting cells. Monoclonal anti-I-A blocking studies showed that both myoglobins are presented in association with the same Ia antigen. Possible explanations for the apparent immunodominance of this antigenic epitope, consisting of residue 109 and nearby residues on the surface of both myoglobins, include a peculiar immunogenicity of the surface topography of this site of a preferred orientation of the molecule imposed by antigen-presenting cells when T cells first encounter the antigen. The latter explanation is related to but distinct from "determinant selection." T-cell recognition of conformation is discussed.

The crystal structures are reported of N-[2-(1-benzenesulfonyl-1H-pyrazol-3-yl)-6-methyl-phenyl]-benzenesulfonamide, 1, and N-[2-(1-toluene-4-sulfonyl-1H-pyrazol-3-yl)-6-methyl-phenyl]-benzenesulfonamide, 2: two compounds used in a recently reported antileishmania study. The crystallographic study reveals significant differences in the conformations adopted by molecules of 1 compared to those adopted by the three independent molecules of 2 in the solid state. The conformation differences between molecules of 1, on one hand, and the three molecules of 2, on the other, are not driven by steric effects within the molecular arrangements. If molecules 2 adopted the molecular conformation found for 1, severe steric interference would occur in the chains and other aggregates generated from the intermolecular contacts. As all the intermolecular interactions are of a weak nature, it is unlikely that aggregation would survive in dilute aqueous media, and hence the steric constraints on the conformations adopted in the solid state would not be in place in solution. Thus the difference in the solid state conformations offers no light on the greater activity of compound 1 compared to that of compound 2 in the antileishmania study in aqueous media.

Stomach contents were analyzed of six pygmy sperm whales (Kogia breviceps) and five dwarf sperm whales (Kogia sima) which were taken as by-catch or were stranded specimens in coastal Taiwan from 1998 through 2000. Twenty-two species in 12 families of oceanic cephalopods were identified. In pygmy sperm whales, Enoploteuthis chunii, Sthenoteuthis oualaniensis, and Taonius pavo were the primary prey in the diet, while E. chunii, Histioteuthis miranda, and T. pavo were the most important prey items ingested by dwarf sperm whales. Although the primary prey items these two species ingested were very similar, each item comprised a different proportion for each whale species. A similarity test demonstrated a significant difference in prey composition, and SIMPER analysis showed that E. chunii was ranked first and contributed 37.1 % to the average dissimilarity between pygmy and dwarf sperm whales. Pygmy sperm whales fed on much larger T. pavo compared to those ingested by dwarf sperm whales, while dwarf sperm whales ingested more H. miranda than did pygmy sperm whales. These results support the view that pygmy sperm whales live seaward of the continental shelf and that dwarf sperm whales live more in coastal waters.

Solution 1D and 2D NMR, together with limited isotope labeling, have led to the assignment of the heme, axial His, and numerous heme contact residues in sperm whale, horse, and human deoxy myoglobin. The paramagnetic relaxivity leads to increased line widths and shorter T1s with little compensation in increased dispersion due to dipolar shifts. Hence only limited, but crucial F helix standard backbone sequence specific assignment could be made for heme cavity residues. Numerous other residues with significant dipolar shifts could be assigned from the characteristic scalar connectivities and dipolar contacts to the heme predicted by the crystal structure. It is concluded that the complete and unambiguous assignment of the heme pyrrole substituent signals is not attainable by 2D NMR alone without either partial deuterium labeling of the heme or parallel assignment of key residues in dipolar contact with the heme; hence the present study revises some earlier assignments. The resulting dipolar shifts for nonligated residues, together with the crystal coordinates of deoxy myoglobin, were used to determine the orientation relative to the heme and the anisotropy of the paramagnetic susceptibility tensor. The significant anisotropy, |Δχ| ∼1 × 10-9 m3/mol, however, is shown to result in dipolar shift with reciprocal square, rather than just reciprocal, absolute temperature dependence, which is indicative of large zero field splitting rather than g-tensor anisotropy. The appropriate equation for a 5B2 ground state allows an estimate of the zero-field splitting, D ∼−10 cm-1, which is in good agreement with earlier results. The present NMR data favor a spin-only magnetic moment with S = 2 and D ∼−10 cm-1 over a ground state with S < 2 and significant orbital contribution (Hendrich and Debrunner, 1989).

Members of the G-protein-coupled receptor superfamily (GPCRs) undergo homo- and/or hetero-oligomerization to induce cell signaling. Although some of these show constitutive activation, it is not clear how such GPCRs undergo homo-oligomerization with transmembrane helix movement. We previously reported that angiotensin II (Ang II) type 2 (AT(2)) receptor, a GPCR, showed constitutive activation and induced apoptosis independent of its ligand, Ang II. In the present study, we analyzed the translocation and oligomerization of the AT(2) receptor with transmembrane movement when the receptor induces cell signaling. Constitutively active homo-oligomerization, which was due to disulfide bonding between Cys(35) in one AT(2) receptor and Cys(290) in another AT(2) receptor, was localized in the cell membrane without Ang II stimulation and induced apoptosis without changes in receptor conformation. These results provide the direct evidence that the constitutively active homo-oligomeric GPCRs by intermolecular interaction in two extracellular loops is translocated to the cell membrane and induces cell signaling independent of receptor conformation and ligand stimulation.