Biophysics and Physicobiology
Online ISSN : 2189-4779
ISSN-L : 2189-4779
Current issue
Displaying 1-16 of 16 articles from this issue
Review Article (Invited)
  • Takashi Fujishiro, Ryosuke Nakamura, Kouhei Kunichika, Yasuhiro Takaha ...
    Article type: Review Article (Invited)
    2022 Volume 19 Article ID: e190001
    Published: 2022
    Released on J-STAGE: February 22, 2022
    Advance online publication: February 08, 2022
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    Cysteine desulfurases are pyridoxal-5'-phosphate (PLP)-dependent enzymes that mobilize sulfur derived from the l-cysteine substrate to the partner sulfur acceptor proteins. Three cysteine desulfurases, IscS, NifS, and SufS, have been identified in ISC, NIF, and SUF/SUF-like systems for iron-sulfur (Fe-S) cluster biosynthesis, respectively. These cysteine desulfurases have been investigated over decades, providing insights into shared/distinct catalytic processes based on two types of enzymes (type I: IscS and NifS, type II: SufS). This review summarizes the insights into the structural/functional varieties of bacterial and eukaryotic cysteine desulfurases involved in Fe-S cluster biosynthetic systems. In addition, an inactive cysteine desulfurase IscS paralog, which contains pyridoxamine-5'-phosphate (PMP), instead of PLP, is also described to account for its hypothetical function in Fe-S cluster biosynthesis involving this paralog. The structural basis for cysteine desulfurase functions will be a stepping stone towards understanding the diversity and evolution of Fe-S cluster biosynthesis.

Regular Article
  • Ryohei Kondo, Kota Kasahara, Takuya Takahashi
    Article type: Regular Article
    2022 Volume 19 Article ID: e190002
    Published: 2022
    Released on J-STAGE: February 22, 2022
    Advance online publication: February 08, 2022
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    Supplementary material

    Elucidating the principles of sequence–structure relationships of proteins is a long-standing issue in biology. The nature of a short segment of a protein is determined by both the subsequence of the segment itself and its environment. For example, a type of subsequence, the so-called chameleon sequences, can form different secondary structures depending on its environments. Chameleon sequences are considered to have a weak tendency to form a specific structure. Although many chameleon sequences have been identified, they are only a small part of all possible subsequences in the proteome. The strength of the tendency to take a specific structure for each subsequence has not been fully quantified. In this study, we comprehensively analyzed subsequences consisting of four to nine amino acid residues, or N-gram (4≤N≤9), observed in non-redundant sequences in the Protein Data Bank (PDB). Tendencies to form a specific structure in terms of the secondary structure and accessible surface area are quantified as information quantities for each N-gram. Although the majority of observed subsequences have low information quantity due to lack of samples in the current PDB, thousands of N-grams with strong tendencies, including known structural motifs, were found. In addition, machine learning partially predicted the tendency of unknown N-grams, and thus, this technique helps to extract knowledge from the limited number of samples in the PDB.

  • Yuka Oka, Shota Ushiba, Naruto Miyakawa, Madoka Nishio, Takao Ono, Yas ...
    Article type: Regular Article
    2022 Volume 19 Article ID: e190003
    Published: 2022
    Released on J-STAGE: February 26, 2022
    Advance online publication: February 09, 2022
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    C-reactive protein (CRP) is an important biomarker of infection and inflammation, as CRP is one of the most prominent acute-phase proteins. CRP is usually detected using anti-CRP antibodies (Abs), where the intermolecular interactions between CRP and the anti-CRP Ab are largely affected by the pH and ionic strength of environmental solutions. Therefore, it is important to understand the environmental effects of CRP–anti-CRP Ab interactions when designing highly sensitive biosensors. Here, we investigated the efficiency of fluorescently labeled CRP–anti-CRP monoclonal antibody (mAb) interactions at different pHs and ionic strengths. Our results indicate that the affinity was insensitive to pH changes in the range of 5.9 to 8.1, while it was significantly sensitive to ionic strength changes. The binding affinity decreased by 55% at an ionic strength of 1.6 mM, when compared to that under a physiological condition (~150 mM). Based on the isoelectric focusing results, both the labeled CRP and anti-CRP mAb were negatively charged in the studied pH range, which rendered the system insensitive to pH changes, but sensitive to ionic strength changes. The decreased ionic strength led to a significant enhancement of the repulsive force between CRP and the anti-CRP mAb. Although the versality of the findings is not fully studied yet, the results provide insights into designing highly sensitive CRP sensors, especially field-effect transistor-based sensors.

Commentary and Perspective
Review Article (Invited)
  • Taro Furubayashi, Norikazu Ichihashi
    Article type: Review Article (Invited)
    2022 Volume 19 Article ID: e190005
    Published: 2022
    Released on J-STAGE: February 26, 2022
    Advance online publication: February 15, 2022
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    How can evolution assemble lifeless molecules into a complex living organism? The emergent process of biological complexity in the origin of life is a big mystery in biology. In vitro evolution of artificial molecular replication systems offers unique experimental opportunities to probe possible pathways of a simple molecular system approaching a complex life-like system. This review focuses on experimental efforts to examine evolvability of molecules in vitro from the pioneering Spiegelman’s experiment to our latest research on an artificial RNA self-replication system. Genetic translation and compartmentalization are shown to enable sustainable replication and evolution. Latest studies are revealing that coevolution of self-replicating “host replicators” and freeloading “parasitic replicators” is crucial to extend evolvability of a molecular replication system for continuous evolution and emergence of diversity. Intense competition between hosts and parasites would have existed even before the origin of life and contributed to generating complex molecular ecosystems. This review article is an extended version of the Japanese article “An in vitro evolutionary journey of an artificial RNA replication system towards biological complexity” published in SEIBUTSU-BUTSURI Vol.61, p.240–244 (2021).”

  • Hiroaki Yokota
    Article type: Review Article (Invited)
    2022 Volume 19 Article ID: e190006
    Published: 2022
    Released on J-STAGE: March 25, 2022
    Advance online publication: March 10, 2022
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    Helicases are nucleic acid-unwinding enzymes involved in the maintenance of genome integrity. Helicases share several “helicase motifs” that are highly conserved amino acid sequences and are classified into six superfamilies (SFs). The helicase SFs are further grouped into two classes based on their functional units. One class that includes SFs 3–6 functions as a hexamer that can form a ring around DNA. Another class that includes SFs 1 and 2 functions in a non-hexameric form. The high homology in the primary and tertiary structures among SF1 helicases suggests that SF1 helicases have a common underlying mechanism. However, two opposing models for the functional unit, monomer and dimer models, have been proposed to explain DNA unwinding by SF1 helicases. This paper briefly describes the classification of helicase SFs and discusses the structural homology and the two opposing non-hexameric helicase models of SF1 helicases by focusing on Escherichia coli SF1 helicase UvrD, which plays a significant role in both nucleotide-excision repair and methyl-directed mismatch repair. This paper reviews past and recent studies on UvrD, including the author's single-molecule direct visualization of wild-type UvrD and a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C), the latter of which was used in genetic and biochemical assays that supported the monomer model. The visualization revealed that multiple UvrDΔ40C molecules jointly unwind DNA, presumably in an oligomeric form, similar to wild-type UvrD. Therefore, single-molecule direct visualization of nucleic acid-binding proteins can provide quantitative and kinetic information to reveal their fundamental mechanisms.

  • Hideaki Yoshimura
    Article type: Review Article (Invited)
    2022 Volume 19 Article ID: e190007
    Published: 2022
    Released on J-STAGE: March 26, 2022
    Advance online publication: March 11, 2022
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    Membrane receptors provide interfaces of various extracellular stimuli to transduce the signal into the cell. Receptors are required to possess such conflicting properties as high sensitivity and noise reduction for the cell to keep its homeostasis and appropriate responses. To understand the mechanisms by which these functions are achieved, single-molecule monitoring of the motilities of receptors and signaling molecules on the plasma membrane is one of the most direct approaches. This review article introduces several recent single-molecule imaging studies of receptors, including the author’s recent work on triple-color single-molecule imaging of G protein-coupled receptors. Based on these researches, advantages and perspectives of the single-molecule imaging approach to solving the mechanisms of receptor functions are illustrated.

Regular Article
  • Damien Simon, Atsushi Mukaiyama, Yoshihiko Furuike, Shuji Akiyama
    Article type: Regular Article
    2022 Volume 19 Article ID: e190008
    Published: 2022
    Released on J-STAGE: April 14, 2022
    Advance online publication: March 30, 2022
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    KaiC is the central pacemaker of the circadian clock system in cyanobacteria and forms the core in the hetero-multimeric complexes, such as KaiB–KaiC and KaiA–KaiB–KaiC. Although the formation process and structure of the binary and ternary complexes have been studied extensively, their disassembly dynamics have remained elusive. In this study, we constructed an experimental system to directly measure the autonomous disassembly of the KaiB–KaiC complex under the condition where the dissociated KaiB cannot reassociate with KaiC. At 30°C, the dephosphorylated KaiB–KaiC complex disassembled with an apparent rate of 2.1±0.3 d–1, which was approximately twice the circadian frequency. Our present analysis using a series of KaiC mutants revealed that the apparent disassembly rate correlates with the frequency of the KaiC phosphorylation cycle in the presence of KaiA and KaiB and is robustly temperature-compensated with a Q10 value of 1.05±0.20. The autonomous cancellation of the interactions stabilizing the KaiB–KaiC interface is one of the important phenomena that provide a link between the molecular-scale and system-scale properties.

Review Article (Invited)
  • Fumiaki Kono, Kazuo Kurihara, Taro Tamada
    Article type: Review Article (Invited)
    2022 Volume 19 Article ID: e190009
    Published: 2022
    Released on J-STAGE: April 16, 2022
    Advance online publication: April 01, 2022
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    Hydrogen atoms and hydration water molecules in proteins are essential for many biochemical processes, especially enzyme catalysis. Neutron crystallography enables direct observation of hydrogen atoms, and reveals molecular recognition through hydrogen bonding and catalytic reactions involving proton-coupled electron transfer. The use of neutron crystallography is still limited for proteins, but its popularity is increasing owing to an increase in the number of diffractometers for structural biology at neutron facilities and advances in sample preparation. According to the characteristics of the neutrons, monochromatic or quasi-Laue methods and the time-of-flight method are used in nuclear reactors and pulsed spallation sources, respectively, to collect diffraction data. Growing large crystals is an inevitable problem in neutron crystallography for structural biology, but sample deuteration, especially protein perdeuteration, is effective in reducing background levels, which shortens data collection time and decreases the crystal size required. This review also introduces our recent neutron structure analyses of copper amine oxidase and copper-containing nitrite reductase. The neutron structure of copper amine oxidase gives detailed information on the protonation state of dissociable groups, such as the quinone cofactor, which are critical for catalytic reactions. Electron transfer via a hydrogen-bond jump and a hydroxide ion ligation in copper-containing nitrite reductase are clarified, and these observations are consistent with the results from the quantum chemical calculations. This review article is an extended version of the Japanese article, Elucidation of Enzymatic Reaction Mechanism by Neutron Crystallography, published in SEIBUTSU-BUTSURI Vol. 61, p.216–222 (2021).

  • Yuhei Tachi, Satoru G. Itoh, Hisashi Okumura
    Article type: Review Article (Invited)
    2022 Volume 19 Article ID: e190010
    Published: 2022
    Released on J-STAGE: April 20, 2022
    Advance online publication: April 02, 2022
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    Alzheimer’s disease is thought to be caused by the aggregation of amyloid-β (Aβ) peptides. Their aggregation is accelerated at hydrophilic/hydrophobic interfaces such as the air–water interface and the surface of monosialotetrahexosylganglioside (GM1) clusters on neuronal cell membranes. In this review, we present recent studies of full-length Aβ (Aβ40) peptides and Aβ(16–22) fragments in such heterogeneous environments by molecular dynamics (MD) simulations. These peptides have both hydrophilic and hydrophobic amino-acid residues and tend to exist at the hydrophilic/hydrophobic interface. Therefore, the peptide concentration increases at the interface, which is one of the factors that promote aggregation. Furthermore, it was found that Aβ40 forms an α-helix structure and then a β-hairpin structure at the interface. The β-hairpin promotes the formation of oligomers with intermolecular β-sheets. It means that not only the high concentration of Aβ40 at the interface but also the structure of Aβ40 itself promotes aggregation. In addition, MD simulations of Aβ40 on recently-developed GM1-glycan clusters showed that the HHQ (13–15) segment of Aβ40 is important for the recognition of GM1-glycan clusters. It was also elucidated that Aβ40 forms a helix structure in the C-terminal region on the GM1-glycan cluster. This result suggests that the helix formation, which is the first step in the conformational changes toward pathological aggregation, is initiated at the GM1-glycan moieties rather than at the lipid-ceramide moieties. These studies will enhance the physicochemical understanding of the structural changes of Aβ at the heterogeneous interfaces and the mechanism of Alzheimer’s disease pathogenesis.

  • Takao K. Suzuki
    Article type: Review Article (Invited)
    2022 Volume 19 Article ID: e190011
    Published: 2022
    Released on J-STAGE: April 20, 2022
    Advance online publication: April 05, 2022
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    Design principles of phenotypes in organisms are fundamental issues in physical biology. So far, understanding “systems” of living organisms have been chiefly promoted by understanding the underlying biomolecules such as genes and proteins, and their intra- and inter-relationships and regulations. After a long period of sophistication, biophysics and molecular biology have established a general framework for understanding ‘molecular systems’ in organisms without regard to species, so that the findings of fly studies can be applied to mouse studies. However, little attention has been paid to exploring “phenotypic systems” in organisms, and thus its general framework remains poorly understood. Here I review concepts, methods, and case studies using butterfly and moth wing patterns to explore phenotypes as systems. First, I present a unifying framework for phenotypic traits as systems, termed multi-component systems. Second, I describe how to define components of phenotypic systems, and also show how to quantify interactions among phenotypic parts. Subsequently, I introduce the concept of the macro-evolutionary process, which illustrates how to generate complex traits. In this point, I also introduce mathematical methods, “phylogenetic comparative methods”, which provide stochastic processes along molecular phylogeny as bifurcated paths to quantify trait evolution. Finally, I would like to propose two key concepts, macro-evolutionary pathways and genotype-phenotype loop (GP loop), which must be needed for the next directions. I hope these efforts on phenotypic biology will become one major target in biophysics and create the next generations of textbooks. This review article is an extended version of the Japanese article, Biological Physics in Phenotypic Systems of Living Organisms, published in SEIBUTSU-BUTSURI Vol. 61, p. 31–35 (2021).

Regular Article
  • Shinjiro Nakahata, Tetsushi Komoto, Masashi Fujii, Akinori Awazu
    Article type: Regular Article
    2022 Volume 19 Article ID: e190012
    Published: 2022
    Released on J-STAGE: April 20, 2022
    Advance online publication: April 05, 2022
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    Supplementary material

    During the repair of double-strand breaks (DSBs) in DNA, active mobilizations for conformational changes in chromosomes have been widely observed in eukaryotes, from yeast to animal and plant cells. DSB-damaged loci in the yeast genome showed increased mobility and relocation to the nuclear periphery. However, the driving forces behind DSB-induced chromatin dynamics remain unclear. In this study, mathematical models of normal and DSB-damaged yeast chromosomes were developed to simulate their structural dynamics. The effects of histone degradation in the whole nucleus and the change in the physical properties of damaged loci due to the binding of SUMOylated repair proteins were considered in the model of DSB-induced chromosomes based on recent experimental results. The simulation results reproduced DSB-induced changes to structural and dynamical features by which the combination of whole nuclear histone degradation and the rigid structure formation of repair protein accumulations on damaged loci were suggested to be primary contributors to the process by which damaged loci are relocated to the nuclear periphery.

Review Article (Invited)
  • Toru Kondo, Yutaka Shibata
    Article type: Review Article (Invited)
    2022 Volume 19 Article ID: e190013
    Published: 2022
    Released on J-STAGE: April 28, 2022
    Advance online publication: April 08, 2022
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    Photosynthetic light-harvesting complexes (LHCs) play a crucial role in concentrating the photon energy from the sun that otherwise excites a typical pigment molecule, such as chlorophyll-a, only several times a second. Densely packed pigments in the complexes ensure efficient energy transfer to the reaction center. At the same time, LHCs have the ability to switch to an energy-quenching state and thus play a photoprotective role under excessive light conditions. Photoprotection is especially important for oxygenic photosynthetic organisms because toxic reactive oxygen species can be generated through photochemistry under aerobic conditions. Because of the extreme complexity of the systems in which various types of pigment molecules strongly interact with each other and with the surrounding protein matrixes, there has been long-standing difficulty in understanding the molecular mechanisms underlying the flexible switching between the light-harvesting and quenching states. Single-molecule spectroscopy studies are suitable to reveal the conformational dynamics of LHCs reflected in the fluorescence properties that are obscured in ordinary ensemble measurements. Recent advanced single-molecule spectroscopy studies have revealed the dynamical fluctuations of LHCs in their fluorescence peak position, intensity, and lifetime. The observed dynamics seem relevant to the conformational plasticity required for the flexible activations of photoprotective energy quenching. In this review, we survey recent advances in the single-molecule spectroscopy study of the light-harvesting systems of oxygenic photosynthesis.

Review Article
  • Etsuro Ito, Kotaro Oka, Fusako Koshikawa
    Article type: Review Article
    2022 Volume 19 Article ID: e190014
    Published: 2022
    Released on J-STAGE: April 28, 2022
    Advance online publication: April 08, 2022
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    Chronic pain often has an unknown cause, and many patients with chronic pain learn to accept that their pain is incurable and pharmacologic treatments are only temporarily effective. Complementary and integrative health approaches for pain are thus in high demand. One such approach is soft touch, e.g., adhesion of pyramidal thorn patches in a pain region. The effects of patch adhesion on pain relief have been confirmed in patients with various types of pain. A recent study using near-infrared spectroscopy revealed that the dorsolateral prefrontal cortex (DLPFC), especially the left side, is likely to be inactivated in patients experiencing pain relief during patch treatment. Mindfulness meditation is another well-known complementary and integrative approach for achieving pain relief. The relation between pain relief due to mindfulness meditation and changes in brain regions, including the DLPFC, has long been examined. In the present review article, we survey the literature describing the effects of the above-mentioned complementary and integrative treatments on pain relief, and outline the important brain regions, including the DLPFC, that are involved in analgesia. We hope that the present article will provide clues to researchers who hope to advance neurosensory treatments for pain relief without medication.

Regular Article
  • Keisuke Inoue, Shoji Takada, Tsuyoshi Terakawa
    Article type: Regular Article
    2022 Volume 19 Article ID: e190015
    Published: 2022
    Released on J-STAGE: May 11, 2022
    Advance online publication: April 14, 2022
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    Supplementary material

    DNA mismatches are frequently generated by various intrinsic and extrinsic factors including DNA replication errors, oxygen species, ultraviolet, and ionizing radiation. These mismatches should be corrected by the mismatches repair (MMR) pathway to maintain genome integrity. In the Escherichia coli (E. coli) MMR pathway, MutS searches and recognizes a base-pair mismatch from millions of base-pairs. Once recognized, ADP bound to MutS is exchanged with ATP, which induces a conformational change in MutS. Previous single-molecule fluorescence microscopy studies have suggested that ADP-bound MutS temporarily slides along double-stranded DNA in a rotation-coupled manner to search a base-pair mismatch and so does ATP-bound MutS in a rotation-uncoupled manner. However, the detailed structural dynamics of the sliding remains unclear. In this study, we performed coarse-grained molecular dynamics simulations of the E. coli MutS bound on DNA in three different conformations: ADP-bound (), ATP-bound open clamp (), and ATP-bound closed clamp () conformations. In the simulations, we observed conformation-dependent diffusion of MutS along DNA. and diffused along DNA in a rotation-coupled manner with rare and frequent groove-crossing events, respectively. In the groove-crossing events, MutS overcame an edge of a groove and temporarily diffused in a rotation-uncoupled manner. It was also indicated that mismatch searches by is inefficient in terms of mismatch checking even though it diffuses along DNA and reaches unchecked regions more rapidly than .

  • Damien Hall, Adam S. Foster
    Article type: Regular Article
    2022 Volume 19 Article ID: e190016
    Published: 2022
    Released on J-STAGE: May 18, 2022
    Advance online publication: April 15, 2022
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    J-STAGE Data Supplementary material

    High speed atomic force microscopy (HS-AFM) is, in principle, capable of yielding nanometer level detail about the surface of static structures. However, for highly dynamic samples HS-AFM may struggle with the correct feature assignment both within and between frames. Feature assignment in HS-AFM is dependent on (i) the intrinsic sampling rate, and (ii) the rate of internal redistribution of the sample. Whilst the first quantity (the sampling rate) is defined by the device parameters, the second quantity is frequently unknown, and is often the desired target of the measurement. This work examines how, even in the absence of gross cell morphological change, the rapid dynamics of living cell membranes, may impose an upper spatial limit to the frame-to-frame assignment of cell micro-topography and other related properties (such as local elasticity) whose motion may be described stochastically. Such a practical maximum may prove useful in the setup of HS-AFM experiments involving dynamic surfaces thereby facilitating selection of the most parsimonious relationship between observation size, image pixilation and sampling rates. To assist with performing the described calculations a graphical user interface-based software package called HS-AFM UGOKU is made freely available.

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