The Molten Globule of β2-Microglobulin Accumulated at pH 4 and Its Role in Protein Folding

The acid transition of β₂-microglobulin (β2m) was studied by tryptophan fluorescence, peptide circular dichroism, and NMR spectroscopy. The protein exhibits a three-state transition with an equilibrium intermediate accumulated at pH 4 (25 °C). The pH 4 intermediate has typical characteristics of the molten globule (MG) state; it showed a native-like secondary structure without specific side-chain tertiary structure, and the hydrodynamic radius determined by pulse field gradient NMR was only 20% larger than that of the native state. The accumulation of the pH 4 intermediate is very analogous to the behavior of apomyoglobin, for which the pH 4 MG has been well characterized, although β2m, a β-protein, is structurally very different from α-helical apomyoglobin. NMR pH titration of histidine residues of β2m has also indicated that His84 has an abnormally low pK_a value in the native state. From the pH dependence of the unfolding transition, the protonations of this histidine and 10 weakly abnormal carboxylates triggered the transition from the native to the MG state. This behavior is again analogous to that of apomyoglobin, suggesting a common mechanism of production of the pH 4 MG. In contrast to the folding of apomyoglobin, in which the MG was equivalent to the burst-phase kinetic folding intermediate, the burst-phase refolding intermediate of β2m, detected by stopped-flow circular dichroism, was significantly more structured than the pH 4 intermediate. It is proposed that the folding of β2m from its acid-denatured state takes place in the following order: denatured state → MG → burst-phase intermediate → native state.     

Native-State Heterogeneity of β2-Microglobulin as Revealed by Kinetic Folding and Real-Time NMR Experiments

The kinetic folding of β₂-microglobulin from the acid-denatured state was investigated by interrupted-unfolding and interrupted-refolding experiments using stopped-flow double-jump techniques. In the interrupted unfolding, we first unfolded the protein by a pH jump from pH 7.5 to pH 2.0, and the kinetic refolding assay was carried out by the reverse pH jump by monitoring tryptophan fluorescence. Similarly, in the interrupted refolding, we first refolded the protein by a pH jump from pH 2.0 to pH 7.5 and used a guanidine hydrochloride (GdnHCl) concentration jump as well as the reverse pH jump as unfolding assays. Based on these experiments, the folding is represented by a parallel-pathway model, in which the molecule with the correct Pro32 cis isomer refolds rapidly with a rate constant of 5–6 s^? 1, while the molecule with the Pro32 trans isomer refolds more slowly (pH 7.5 and 25 °C). At the last step of folding, the native-like trans conformer produced on the latter pathway isomerizes very slowly (0.001–0.002 s^? 1) into the native cis conformer. In the GdnHCl-induced unfolding assays in the interrupted refolding, the native-like trans conformer unfolded remarkably faster than the native cis conformer, and the direct GdnHCl-induced unfolding was also biphasic, indicating that the native-like trans conformer is populated at a significant level under the native condition. The one-dimensional NMR and the real-time NMR experiments of refolding further indicated that the population of the trans conformer increases up to 7–9% under a more physiological condition (pH 7.5 and 37 °C).     

Morphological and genetic relationship of two closely‐related giant water bugs: Appasus japonicus Vuillefroy and Appasus major Esaki (Heteroptera: Belostomatidae)

The East Asian giant water bug species Appasus japonicus Vuillefroy and Appasus major Esaki are aquatic hemipteran insects whose ranges overlap, particularly in the Japanese Archipelago and on the Korean Peninsula. In rare cases, the two species co‐occur. Furthermore, they are very similar ecologically and also morphologically, making their identification extremely difficult, and the possibility of hybridization has also been suggested. In the present study, we re‐examined their taxonomic validity, and the characteristics useful for identifying them. To re‐examine the morphological traits useful for distinguishing these two species, 222 specimens of A. japonicus collected from Japan, Korea, and China, and 132 specimens of A. major from Japan and Korea, were examined. We also performed molecular phylogenetic analyses based on the mitochondrial DNA 16S rRNA and cytochrome oxidase subunit I (COI) regions and the nuclear DNA Histone 3 region. Although the two species are very similar ecologically and also morphologically, they showed significant genetic differentiation. Thus, there is likely some form of reproductive isolation acting between them. Major morphological characteristics overlap extensively between A. japonicus and A. major, and no particular trait was identified as being effective for differentiating these species. All the morphological characteristics examined overlapped between A. japonicus and A. major. However, a principal component analysis based on all of the morphological characteristics revealed that, despite the overlap between these species, it was possible to morphologically distinguish them. Therefore, a more accurate identification becomes possible using multiple characteristics rather than a single characteristic. The male genital paralobes, evaluated as the most useful morphological characteristic, was effective with 100% probability for the Japanese Appasus species. However, for the Asian (i.e. Korean) specimens, this characteristic was not useful. On the other hand, the results of molecular phylogenetic analyses based on the mitochondrial DNA 16S rRNA and COI regions and the nuclear DNA Histone 3 region clearly showed significant genetic differentiation between the two species. Notably, the results for the mitochondrial COI region strongly supported the independence of each monophyletic group (i.e. validity of each species). Therefore, DNA barcoding based on the mitochondrial DNA COI region is also considered useful for the identification of A. japonicus and A. major. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 615–643.     

Technical note: Quantification of neurocranial shape variation using the shortest paths connecting pairs of anatomical landmarks

Three‐dimensional geometric morphometric techniques have been widely used in quantitative comparisons of craniofacial morphology in humans and nonhuman primates. However, few anatomical landmarks can actually be defined on the neurocranium. In this study, an alternative method is proposed for defining semi‐landmarks on neurocranial surfaces for use in detailed analysis of cranial shape. Specifically, midsagittal, nuchal, and temporal lines were approximated using Bezier curves and equally spaced points along each of the curves were defined as semi‐landmarks. The shortest paths connecting pairs of anatomical landmarks as well as semi‐landmarks were then calculated in order to represent the surface morphology between landmarks using equally spaced points along the paths. To evaluate the efficacy of this method, the previously outlined technique was used in morphological analysis of sexual dimorphism in modern Japanese crania. The study sample comprised 22 specimens that were used to generate 110 anatomical semi‐landmarks, which were used in geometric morphometric analysis. Although variations due to sexual dimorphism in human crania are very small, differences could be identified using the proposed landmark placement, which demonstrated the efficacy of the proposed method. Am J Phys Anthropol 151:658–666, 2013. © 2013 Wiley Periodicals, Inc.     

Mutations in SERPINB7, Encoding a Member of the Serine Protease Inhibitor Superfamily,Cause Nagashima-type Palmoplantar Keratosis

“Nagashima-type” palmoplantar keratosis (NPPK) is an autosomal recessive nonsyndromic diffuse palmoplantar keratosis characterized by well-demarcated diffuse hyperkeratosis with redness, expanding on to the dorsal surfaces of the palms and feet and the Achilles tendon area. Hyperkeratosis in NPPK is mild and nonprogressive, differentiating NPPK clinically from Mal de Meleda. We performed whole-exome and/or Sanger sequencing analyses of 13 unrelated NPPK individuals and identified biallelic putative loss-of-function mutations in SERPINB7, which encodes a cytoplasmic member of the serine protease inhibitor superfamily. We identified a major causative mutation of c.796C>T (p.Arg266^∗) as a founder mutation in Japanese and Chinese populations. SERPINB7 was specifically present in the cytoplasm of the stratum granulosum and the stratum corneum (SC) of the epidermis. All of the identified mutants are predicted to cause premature termination upstream of the reactive site, which inhibits the proteases, suggesting a complete loss of the protease inhibitory activity of SERPINB7 in NPPK skin. On exposure of NPPK lesional skin to water, we observed a whitish spongy change in the SC, suggesting enhanced water permeation into the SC due to overactivation of proteases and a resultant loss of integrity of the SC structure. These findings provide an important framework for developing pathogenesis-based therapies for NPPK.