Editors’ Roundup: June 2022

Abstract

This Commentary describes the June 2022 installment of the “Editors’ Roundup” feature. The Editors’ Roundup is a multi-author collective description of recently published biophysical research contributed by editorial board members of different journals with a bonafide interest in publishing biophysical content. This Commentary contains a series of personal recommendations for articles appearing in the following journals, Biophysics and Physicobiology, European Biophysics Journal, Cell Biochemistry and Biophysics, and Biophysical Reviews.

Biophysical Reviews is the sole publishing instrument of IUPAB, the International Union for Pure and Applied Biophysics (IUPAB 2022). As an affiliate of the International Science Council (ISC 2022), IUPAB seeks to act as a positive advocacy body for the international promotion of biophysics at the teaching, research, and development levels. Due to its direct association with IUPAB (and indirectly with the ISC), Biophysical Reviews shares this interest in promoting biophysical research on an international stage. In partial support of this goal the journal has created a regular commentary feature known as the “Editor’s Roundup” (Shearwin et al. 2022) which is intended to be used as a platform for the promotion of published research by representatives of any legitimate commercial or society-based journal with a genuine interest in publishing biophysics-based content.

To contribute to the “Editors’ Roundup” any listed member of a journal’s Editorial Board may submit a short description (less than 300 words) of up to five articles chosen from among their journal’s recent publications (within the last 2 years). Prior to publication all contributions are assembled into the Editors’ Roundup commentary with shared authorship. Those interested in contributing are requested to make contact with either the professional officers of the journal, or the senior members of the Editorial Board, for particular deadlines associated with any of the six issues published each year.

The current Editors’ Roundup commentary contains contributions from four different journals, with these arranged into sections based on the contributor and journal.

European Biophysics Journal

Publisher: Springer-Nature

Web: https://link.springer.com/journal/249

Contributor: Trushar Patel (Editor)

The European Biophysics Journal (EBJ) was first published in 1974 and is the official journal for EBSA (European Biophysical Societies Association). Defining biophysics as the study of biological phenomena using physical methods and concepts, the journal publishes eight issues a year with each issue consisting of a mixture of original papers, review articles, and short letters. In responding to this invitation to describe some publications recently appearing within the EBJ, I decided to place a focus on three articles appearing in a recent Special Issue (SI) (Issue 2, 2021) titled “Multicomponent Lipid Membranes—How molecular organisation leads to function” that was collated and organized by the four Issue Editors, Bert de Groot, Andreas Janshoff, Claudia Steinem, and Markus Zweckstetter.

The first article selected from this SI, the Editorial (de Groot et al. 2021), provides a nice overview of both, the impetus for the SI and the articles appearing within it. The motivation for the SI was the presentation of research progress funded by a multi-year/multi-team granting scheme named Sonderforschungsbereich 803 (provided by the Deutsche Forschungsgemeinschaft). This scheme supported 19 different projects, all aimed at providing molecular level descriptions, using experimental, computational, and theoretical approaches, of the interactions occurring between the many different lipids and proteins in cellular membranes. After describing the goals and rationale for the project, the editorial goes on to provide a short overview of the 14 reviews and original papers appearing within the SI (contributed by the project members). Of these, I would like to bring attention to the articles by Smirnova and Müller (2021) and Risselada and Grubmüller (2021), respectively an original paper and a review article, dealing with different aspects of membrane deformation and fusion—essential processes in vesicular transport mechanisms, cell fusion, and enveloped viral infection.

The selected original paper (Smirnova and Müller 2021) describes steered coarse-grained molecular dynamics (MD) simulations exploring the determinants of the initial association between two bilayer vesicular structures to form the hour-glass hemi-fusion intermediate. Tracing the minimum free-energy path (MFEP), the authors explored the role that membrane curvature plays in facilitating membrane hemi-fusion. Breaking the initial stages of fusion into membrane approach (apposition) and stalk formation, an umbrella sampling bias was applied to the coarse-grained MARTINI MD simulations to establish the importance of curvature (of both membranes) in generating the hemi-fusion intermediate (Smirnova and Müller 2021).

The chosen review article (Risselada and Grubmüller 2021) presented a range of computer simulation and experimental results on the proteins and lipids assisting with membrane fusion. Contrasting the different roles of SNARE proteins in eukaryotes and the various classes of viral fusion proteins, this review details the common/uncommon aspects of membrane fusion associated with apposition, creation of an initial stalk, and subsequent formation of the hemi-fusion intermediate and eventual fusion pore. Read together, the paper by Smirnova and Müller (2021) and the review article by Risselada and Grubmüller (2021) provide both an interesting, and deep, insight into the biophysical factors influencing this essential biological process.

Biophysics and Physicobiology

Publisher: Biophysical Society of Japan

Web:https://www.biophys.jp/biophysics_and_physicobiology.html

Contributor: Haruki Nakamura (Chief Editor)

Biophysics and Physicobiology (BPPB) was initially established in 2005 under the title “Biophysics” before changing its name to BPPB in 2016. BPPB is one of two journals owned and operated by the Biophysical Society of Japan, the other being the Japanese language biophysical journal “Seibutsu Butsuri” (literally Biological Physics). BPPB represents the BSJ’s flagship English language journal and in this role publishes a range of original and review articles across the spectrum of physically oriented biology (~ physicobiology). BPPB is an online journal whereby articles are published and indexed according to their date of acceptance. For this edition of the Editors’ Roundup, the BPPB Editorial Board has chosen four articles that were the awardees of the 9th BPPB Editors’ Choice Award, selected from about 40 articles published in 2021.

• (i)The paper by Ryo Yoshizawa et al. (based in RIKEN) studied the regulation of GRB2 recruitment under the SHC (Src homology 2 domain containing) pathway, using single molecule imaging and fluorescence correlation spectroscopy in living cells. The authors find that a particular pathway operates to regulate the dynamics of the GRB2 signaling activation of RAS, which is a key mechanism for cell fate changes (Yoshizawa et al. 2021).
• (ii)Ryota Kojima and Takashi Yoshidome (Tohoku University) proposed their own measure to identify preferred particle orientations in cryo-electron microscopy data (Kojima and Yoshidome 2021). From their simulations for cryo-EM experiment of a protein, they found that the geometry of the manifold projected onto a two-dimensional space for the protein adopting a preferred biomolecular orientation was significantly different from that adopting a uniformly random orientation.
• (iii)The BPPB invited a review article by Masayuki Oda (Kyoto Prefectural University) (Oda 2021), who studied the structure and function of a cutinase enzyme, useful for the degradation of PET (polyethylene terephthalate) into monomers. His group has succeeded in designing a new multiple point mutant with desired properties, such as high thermostability and high degradative activity, based on knowledge obtained from X-ray crystal structure, thermal measurement, molecular dynamics simulation, and RISM calculations (Oda et al. 2018).
• (iv)The invited review article by Katsumasa Irie from Nagoya University summarizes the advances of the structural and functional studies for ancestral prokaryotic cation channels (Irie 2021). In particular, his group recently discovered a CaV (Voltage-dependent Ca2+ channels)-like channel in a bacterium (Shimomura et al. 2020), and in this review article he proposes a general Ca2+ selectivity mechanism conserved from prokaryotes to eukaryotes.

Cell Biochemistry and Biophysics

Publisher: Springer-Nature

Web: https://www.springer.com/journal/12013

Contributor: Lawrence Berliner (Chief Editor)

Established in 1979, the original and continuing aim of Cell Biochemistry and Biophysics (CBB) is to publish both primary research and review articles capable of increasing our collective understanding of the biochemical and biophysical mechanisms underlying the control (and perturbation) of cellular homeostasis at the cell to tissue level of observation. In this edition of the Biophysical Reviews’ “Editors’ Roundup,” I would like to describe, in some detail, a single recent article that nicely demonstrates this aspect of CBB’s research focus.

The last 20 years have seen a growing scientific appreciation of the effects on cellular processes (such as respiration, signaling, and differentiation) caused by introducing a third spatial dimension (3D) to the arrangement of growing cells (such as that occurring in biological tissue or 3D cell culture models) as opposed to the more traditional two-dimensional (2D) cell culture arrangements favored in early research approaches. Such 3D spatial effects have been shown to be particularly important in determining the developmental fate of cells within cancerous tumors. In line with this area of research the paper I have selected, Badea et al. (2022) investigated the role of initial cell density on the generation of multi-cellular tumor spheroid (MCTS) models created using the hanging drop method. Employing the triple negative breast cancer cell line MDA-MB-231, biophysical analysis was performed on the three-dimensional MCTS cell culture model over a 6-day period with quantitative recording of three-dimensional spheroid morphology and positional measrement of cell viability (via lactate dehydrogenase assay) and hypoxia (via indirect measurement of the protein expression levels of protective markers and transcription factors). Using a range of different solution cell densities at the initial stage of creating the hanging drop, the authors have created a set of well-defined and well-characterized MCTS culture systems that exhibit different levels of cellular viability and proliferation (Badea et al. 2022).

Biophysical Reviews

Type: Springer-Nature and IUPAB.

Web: https://www.springer.com/journal/12551

Contributor: Kuniaki Nagayama (Executive Editor)

As an Executive Editor of the journal, I have been asked to comment on a number of recently published articles appearing in Biophysical Reviews. In making this personal recommendation, I have chosen articles appearing within the recently published Special Issue based on the 20^th IUPAB Congress held virtually Sao Paulo Brazil (Itri et al. 2021; Hall 2021). Among the 30 review articles appearing within this issue, I have chosen to highlight the following four articles.

• (i).Cryogenic super-resolution correlative light and electron microscopy on the frontier of subcellular imaging (Tian et al. 2021): Correlative light and electron microscopy (CLEM) is an ideal imaging method that combines the complementary advantages of electron microscopy (EM) and fluorescence microscopy (FM); the former can visualize the structure of a target at high resolution and the latter pinpoints the location of the target. In this review article, the authors focused onto the resolution gap still lying between EM and FM and describe how this gap may be filled by upgrading FM through the introduction of single molecule light microscopy (SMLM) such as PALM or STORM (Tian et al. 2021).
• (ii).Advances in nonlinear optical microscopy techniques for in vivo and in vitro neuroimaging (Pallen et al. 2021): Understanding the mechanism of the brain via the use of optical microscopy is one of the great remaining challenges in neuroimaging. Recent advances in optical microscopy techniques have evolved to produce powerful tools to overcome the scattering of light and provide improved in vivo neuroimaging with subcellular resolution and high penetration depth. In this review article, the authors focused on these types of microscopy techniques (able to overcome such scattering limitations) including two-photon and three-photon fluorescence, second-harmonic generation, third-harmonic generation, coherent anti-Stokes Raman scattering, and stimulated Raman scattering (Pallen et al. 2021).
• (iii).Insights into lipid-protein interactions from computer simulations (Tieleman et al. 2021): Molecular dynamics (MD) simulations, conducted using both standard atomistic models and sophisticated large-scale models, have now reached time and length scales that allow for meaningful investigations of membrane systems of direct biological and biomedical interest. In this review article, the authors have described MD studies of localized lipid composition emanating from ten different eukaryotic membrane proteins embedded in a plasma membrane mixture with more than 60 different lipid types and found that each protein will generate its own environment, distinctly different from the lipid concentrations in the bulk. Particularly interesting were the descriptions of non-uniform perturbations of local membrane properties described for G protein-coupled receptors (GPCRs) (Tieleman et al. 2021).
• (iv).Protein conformational dynamics and phenotypic switching (Kulkarni et al. 2021): Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure but exist as conformational ensembles. The protein interactions between IDPs and their multiple partners form scale-free protein interaction networks (PINs) that facilitate information flow in the cell. In this review, the authors have focused on the significance of IDP conformational dynamics in the non-genetic mechanisms of phenotypic switching in cells (Kulkarni et al. 2021).

Concluding remarks

This commentary is the second in the continuing “Editors’ Roundup” series run by the IUPAB journal “Biophysical Reviews.” This commentary format is aimed at providing an international platform for describing recently published biophysical content from a diverse range of publishing sources. Descriptions are provided by Members of the Editorial Boards of the different journals and carry with them information about the nature of the journal and its particular area of interest. Any parties interested in participating (having a real association with a journal that publishes biophysical content) are asked to make contact with either the professional officers of the Biophysical Reviews journal or a senior member of the Editorial Board.

Declarations

Conflict of interest

The authors declare no competing interests.