Classification and annotation of the relationship between protein structural change and ligand binding

The causal relationship between protein structural change and ligand binding was classified and annotated for 839 nonredundant pairs of crystal structures in the Protein Data Bank—one with and the other without a bound low-molecular-weight ligand molecule. Protein structural changes were first classified into either domain or local motions depending on the size of the moving protein segments. Whether the protein motion was coupled with ligand binding was then evaluated based on the location of the ligand binding site and by application of the linear response theory of protein structural change. Protein motions coupled with ligand binding were further classified into either closure or opening motions. This classification revealed the following: (i) domain motions coupled with ligand binding are dominated by closure motions, which can be described by the linear response theory; (ii) local motions frequently accompany order-disorder or α-helix-coil conformational transitions; and (iii) transferase activity (Enzyme Commission   number 2) is the predominant function among coupled domain closure motions. This could be explained by the closure motion acting to insulate the reaction site of these enzymes from environmental water.     

Dominant induction of vaccine antigen-specific cytotoxic T lymphocyte responses after simian immunodeficiency virus challenge

Cytotoxic T lymphocyte (CTL) responses are crucial for the control of human and simian immunodeficiency virus (HIV and SIV) replication. A promising AIDS vaccine strategy is to induce CTL memory resulting in more effective CTL responses post-viral exposure compared to those in natural HIV infections. We previously developed a CTL-inducing vaccine and showed SIV control in some vaccinated rhesus macaques. These vaccine-based SIV controllers elicited vaccine antigen-specific CTL responses dominantly in the acute phase post-challenge. Here, we examined CTL responses post-challenge in those vaccinated animals that failed to control SIV replication. Unvaccinated rhesus macaques possessing the major histocompatibility complex class I haplotype 90-088-Ij dominantly elicited SIV non-Gag antigen-specific CTL responses after SIV challenge, while those induced with Gag-specific CTL memory by prophylactic vaccination failed to control SIV replication with dominant Gag-specific CTL responses in the acute phase, indicating dominant induction of vaccine antigen-specific CTL responses post-challenge even in non-controllers. Further analysis suggested that prophylactic vaccination results in dominant induction of vaccine antigen-specific CTL responses post-viral exposure but delays SIV non-vaccine antigen-specific CTL responses. These results imply a significant influence of prophylactic vaccination on CTL immunodominance post-viral exposure, providing insights into antigen design in development of a CTL-inducing AIDS vaccine.     

Automatic analysis of composite physical signals using non-negative factorization and information criterion

In time-resolved spectroscopy, composite signal sequences representing energy transfer in fluorescence materials are measured, and the physical characteristics of the materials are analyzed. Each signal sequence is represented by a sum of non-negative signal components, which are expressed by model functions. For analyzing the physical characteristics of a measured signal sequence, the parameters of the model functions are estimated. Furthermore, in order to quantitatively analyze real measurement data and to reduce the risk of improper decisions, it is necessary to obtain the statistical characteristics from several sequences rather than just a single sequence. In the present paper, we propose an automatic method by which to analyze composite signals using non-negative factorization and an information criterion. The proposed method decomposes the composite signal sequences using non-negative factorization subjected to parametric base functions. The number of components (i.e., rank) is also estimated using Akaike's information criterion. Experiments using simulated and real data reveal that the proposed method automatically estimates the acceptable ranks and parameters.     

A bootstrap method for testing equality of peak months

When ecological traits differ seasonally among biological groups, environmental adaptation is expected. However, current analytical methods for such seasonal data ignore the circular nature of data and therefore are likely to be flawed. We propose a simple bootstrap hypothesis test which statistically quantifies the presence/absence of differences in peak months for multiple groups taking the circular nature of the data into account. The test is based on a robust distribution-free method. Simulations showed that the test gives a satisfactory performance. The test is illustrated using data for anchovy and sardine egg abundances in the western North Pacific.     

Dehydration polycondensation of dicarboxylic acids and diols using sublimating strong brønsted acids

We investigated catalytic activities of strong br?nsted acids for dehydration polycondensations of dicarboxylic acids and diols, which were carried out at low temperature (<100 °C) under reduced pressure (0.3-3 mmHg). Strong Br?nsted acids, bis(perfluoroalkanesulfonyl)imide and perfluoroalkanesulfonic acid, showed higher activity than p-toluenesulfonic acid or rare-earth catalysts at 60 °C. In particular, bis(nonafluorobutanesulfonyl)imide (Nf(2)NH) showed the highest activity to synthesize not only aliphatic polyester (M(n) > 19000) but also aromatic polyester (M(n) > 7000). The used Nf(2)NH was sublimated from the reaction flask during polycondensation, and the sublimate, Nf(2)NH, was extra pure so that we can reuse the catalyst without loss of the activity in the dehydration polycondensations.     

Proteases are associated with a minor fucoxanthin chlorophyll a/c-binding protein from the diatom,Chaetoceros gracilis

We previously showed that most subunits in the oxygen-evolving photosystem II (PSII) preparation from the diatom Chaetoceros gracilis are proteolytically unstable. Here, we focused on identifying the proteases that cleave PSII subunits in thylakoid membranes. Major PSII subunits and fucoxanthin chlorophyll (Chl) a/c‐binding proteins (FCPs) were specifically degraded in thylakoid membranes. The PSI subunits, PsaA and PsaB, were slowly degraded, and cytochrome f was barely degraded. Using zymography, proteolytic activities for three metalloproteases (116, 83, and 75 kDa) and one serine protease (156 kDa) were detected in thylakoid membranes. Two FCP fractions (FCP-A and FCP-B/C) and a photosystem fraction were separated by sucrose gradient centrifugation using dodecyl maltoside‐solubilized thylakoids. The FCP-A fraction featured enriched Chl c compared with the bulk of FCP-B/C. Zymography revealed that 116, 83, and 94 kDa metalloproteases were mostly in the FCP-A fraction along with the 156 kDa serine protease. When solubilized thylakoids were separated with clear-native PAGE, zymography detected only the 83 kDa metalloprotease in the FCP-A band. Because FCP-A is selectively associated with PSII, these FCP-A-associated metalloproteases and serine protease may be responsible for the proteolytic degradation of FCPs and PSII in thylakoid membranes.     

Functional dynamics of SARS-CoV-2 3C-like protease as a member of clan PA

SARS-CoV-2 3C-like protease (3CL^pro), a potential therapeutic target for COVID-19, consists of a chymotrypsin fold and a C-terminal α-helical domain (domain III), the latter of which mediates dimerization required for catalytic activation. To gain further understanding of the functional dynamics of SARS-CoV-2 3CL^pro, this review extends the scope to the comparative study of many crystal structures of proteases having the chymotrypsin fold (clan PA of the MEROPS database). First, the close correspondence between the zymogen-enzyme transformation in chymotrypsin and the allosteric dimerization activation in SARS-CoV-2 3CL^pro is illustrated. Then, it is shown that the 3C-like proteases of family Coronaviridae (the protease family C30), which are closely related to SARS-CoV-2 3CL^pro, have the same homodimeric structure and common activation mechanism via domain III mediated dimerization. The survey extended to order Nidovirales reveals that all 3C-like proteases belonging to Nidovirales have domain III, but with various chain lengths, and 3CL^pro of family Mesoniviridae (family C107) has the same homodimeric structure as that of C30, even though they have no sequence similarity. As a reference, monomeric 3C proteases belonging to the more distant family Picornaviridae (family C3) lacking domain III are compared with C30, and it is shown that the 3C proteases are rigid enough to maintain their structures in the active state.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12551-022-01020-x.     

Water temperature sampling by foraging Brünnich's Guillemots with bird-borne data loggers

We describe the features of waters where seabirds were feeding by sampling vertical water temperature profiles with data loggers mounted on five Brünnich's Guillemots in Svalbard, Norway. The guillemots foraged in a cold water (−0.5–0.5°C SST (sea surface temperature)) by making 1.8 dive bouts in short trips (32–257 min duration) as well as in moderate (0.5–2.0°C SST) and warm waters (2.5–4.0°C SST) by making 6.0 dive bouts during long trips (411–688 min duration). Judging from outbound flying time (15.7–24.4 min), time between dive bouts (23.9–43.3 min) and water types, the birds probably fed in fjord or coastal waters during short trips and in both coastal and offshore waters during long trips. Water temperature and diving behaviour can be simultaneously recorded by small data loggers, which therefore will provide useful information on marine features and foraging activity of top predators.