Biology subjects

Nagae, T.

Publications and source records attributed to Nagae, T..

5 recordsLinked to original sources

bioRxiv2026

zsasa: a Zig-based engine for high-throughput solvent accessible surface area at proteome scale

Solvent accessible surface area (SASA) is widely used to describe protein stability, ligand binding, mutation effects, and protein-protein interfaces. As structural biology workloads expand to predicted-structure col-lections, trajectories, and large assemblies, SASA tools must combine reproducible calculation with high throughput, low memory use, and workflow-friendly input handling. We present zsasa, a Zig-based SASA engine with command-line and Python interfaces. zsasa implements the established Shrake-Rupley and Lee-Richards algorithms, provides exact f64/f32 modes and an optional bitmask approximation, and supports batch and trajectory workflows, compressed structure inputs, and configurable atom classification including Chemical Component Dictionary (CCD)-based radii for non-standard components. In matched Shrake-Rupley validation on 4,370 Escherichia coli AlphaFold Database structures, exact double-precision zsasa reproduced FreeSASA total SASA values to near numerical identity. In 10-thread batch benchmarks on the E. coli and 23,586-structure human AlphaFold collections, zsasa achieved a 2.94-fold speedup over a FreeSASA batch wrapper in exact f64 mode. In bitmask mode, zsasa reached up to a 9.70-fold speedup, using roughly 12.5% to 25% of the comparator peak memory. Trajectory benchmarks exceeded 1,000 frames/s at tens of megabytes of peak memory, and a 4.5-million-atom PDB stress-test file completed in less than 5 s. These results support zsasa as a practical tool for reproducible, low-memory generation of surface-derived structural features at large scale. zsasa is available under the MIT License at https://github.com/N283T/zsasa.

bioinformatics↗

bioRxiv2026

Prolonged cold exposure enhances regeneration potential in Arabidopsis

Prolonged cold exposure over winter impacts plant growth and development but its role beyond flowering regulation remains underexplored. In this study, we show that extended cold enhances regenerative capacity, promoting both callus formation and shoot regeneration in Arabidopsis. This enhancement is mediated by the cold-induced AP2/ERF transcription factors C-REPEAT/DRE-BINDING FACTOR 1 (CBF1), CBF2 and CBF3 which interact with the histone acetyltransferase HISTONE ACETYLTRANSFERASE OF THE GNAT FAMILY 1 (HAG1). The CBFs recruit HAG1 to the loci of key regeneration regulators, such as WUSCHEL-RELATED HOMEOBOX 5 (WOX5), to promote their expression via histone acetylation. Our findings thus uncover an epigenetic mechanism by which prolonged cold primes plants for enhanced regeneration, highlighting how environmental cues influence developmental plasticity in plants.

plant biology↗

bioRxiv2025

Global Identification of Highly Expandable and Shrinkable Proteins via Intramolecular Distance Scoring Analysis

Experimental and analytical characterizations of protein structural changes are essential for understanding various biological functions. It is well known that each protein or protein complex undergoes shape changes in a specific manner and to a certain extent, influenced by factors such as molecular interactions and the solvent environment. To enable quantitative comparisons of shape changes among multiple proteins, we previously introduced an index called the "UnMorphness Factor" (UMF), which is derived using a simple, original method-- intramolecular distance scoring analysis (DSA). Using this approach, we have accumulated data for over 15,000 proteins. Here, we show that among the proteins exhibiting significant structural changes, some are found to undergo substantial isotropic volume expansion or contraction. The uniformity of three-dimensional size changes can be represented by a linear correlation between the average and standard deviation of all intramolecular C-C distances across a proteins structural set. Packing analysis of such proteins reveals that the void volume within the same polypeptide chain can increase by up to 50% relative to the reference state. Our study clearly demonstrates that this type of structural change plays a crucial role in understanding the detailed processes of ligand binding, catalytic reaction cycles, and protein folding pathways.

biophysics↗

bioRxiv2024

Protonation/deprotonation-driven switch for the redox stability of low-potential ferredoxin

Ferredoxin is a small iron-sulfur protein and acts as an electron carrier. Low-potential ferredoxins harbor [4Fe-4S] cluster(s), which play(s) a crucial role as the redox center. Low-potential ferredoxins are able to cover a wide range of redox potentials (-700 to -200 mV); however, the mechanisms underlying the factors which control the redox potential are still enigmatic. Here, we determined the neutron structure of ferredoxin from Bacillus thermoproteolyticus, and experimentally revealed the exact hydrogen-bonding network involving the [4Fe-4S] cluster. The density functional theory calculations based on the hydrogen-bonding network revealed that protonation states of the sidechain of Asp64 close to the [4Fe-4S] cluster critically affected the stability of the reduced state in the cluster. These findings provide the first identification of the intrinsic control factor of redox potential for the [4Fe-4S] cluster in low-potential ferredoxins.

biochemistry↗

bioRxiv2020

Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

Cyanobacteriochromes (CBCRs) are bilin-binding photosensors of the phytochrome superfamily that show remarkable spectral diversity. The green/red CBCR subfamily is important for regulating chromatic acclimation of photosynthetic antenna in cyanobacteria and is applied for optogenetic control of gene expression in synthetic biology. They are suggested to combine the bilin C15-Z/C15-E photoisomerization with a change in the bilin protonation state to drive their absorption changes. However, structural information and direct evidence of the bilin protonation state are lacking. Here we report a high-resolution (1.63[A]) crystal structure of the bilin-binding domain of the chromatic acclimation sensor RcaE in the red-absorbing photoproduct state. The bilin is buried within a "pan" consisting of hydrophobic residues, where the bilin configuration/conformation is C5-Z,syn/C10-Z,syn/C15-E,syn with the A-C rings co-planar and the D-ring tilted. Three pyrrole nitrogens of the A-C rings are covered in the -face with a hydrophobic lid of Leu249 influencing the bilin pKa, whereas they are directly hydrogen-bonded in the {beta}-face with the carboxyl group of Glu217. Glu217 is further connected to a cluster of waters forming a hole in the pan, which are in exchange with solvent waters in molecular dynamics simulation. We propose that the "holey pan" structure functions as a proton-exit/influx pathway upon photoconversion. NMR analysis demonstrated that the four pyrrole nitrogen atoms are indeed fully protonated in the red-absorbing state, but one of them, most likely the B-ring nitrogen, is deprotonated in the green-absorbing state. These findings deepen our understanding of the diverse spectral tuning mechanisms present in CBCRs. Significance StatementGreen/red CBCRs are one of the most important CBCR subfamilies owing to their physiological roles in cyanobacteria phylum and optogenetic applications. They are known to utilize a change in the bilin protonation state to drive the marked change in green/red absorption, but the structural basis of the protochromic green/red photocycle are not well understood. Here, we have determined the crystal structure of the chromatic acclimation sensor RcaE of this subfamily in the photoproduct state, demonstrating a unique conformation of the bilin and its interacting residues. In addition, we provide direct evidence of the protonation state of the bilin via NMR analysis. These findings bring insight to our understanding of the molecular mechanisms underlying the spectral diversity of CBCRs.

biochemistry↗