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Автор: Grafiati

Опубліковано: 6 вересня 2023

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1

Joshi, Prakash, and Partha Pratim Mondal. "Single-Molecule Clustering for Super-Resolution Optical Fluorescence Microscopy." Photonics 9, no. 1 (December 24, 2021): 7. http://dx.doi.org/10.3390/photonics9010007.

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Molecular assembly in a complex cellular environment is vital for understanding underlying biological mechanisms. Biophysical parameters (such as single-molecule cluster density, cluster-area, pairwise distance, and number of molecules per cluster) related to molecular clusters directly associate with the physiological state (healthy/diseased) of a cell. Using super-resolution imaging along with powerful clustering methods (K-means, Gaussian mixture, and point clustering), we estimated these critical biophysical parameters associated with dense and sparse molecular clusters. We investigated Hemaglutinin (HA) molecules in an Influenza type A disease model. Subsequently, clustering parameters were estimated for transfected NIH3T3 cells. Investigations on test sample (randomly generated clusters) and NIH3T3 cells (expressing Dendra2-Hemaglutinin (Dendra2-HA) photoactivable molecules) show a significant disparity among the existing clustering techniques. It is observed that a single method is inadequate for estimating all relevant biophysical parameters accurately. Thus, a multimodel approach is necessary in order to characterize molecular clusters and determine critical parameters. The proposed study involving optical system development, photoactivable sample synthesis, and advanced clustering methods may facilitate a better understanding of single molecular clusters. Potential applications are in the emerging field of cell biology, biophysics, and fluorescence imaging.

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2

Goñi, Félix M. "Birth and Early Steps of the Organization of Biophysics in Spain." Biophysica 2, no. 4 (November 19, 2022): 498–505. http://dx.doi.org/10.3390/biophysica2040042.

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In the 1960s, Biophysics was an unheard of scientific field in Spain, and even outside Spain, the distinction between Biophysics and Molecular Biology was not clear at the time. This paper describes briefly the developments that led to the foundation of the Spanish National Committee for Biophysics (1981) and of the Spanish Biophysical Society (1987), the incorporation of Spain into IUPAB and EBSA, and the normalized presence of Biophysics as a compulsory subject in undergraduate curricula in Spain.

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3

Leake, Mark C. "The physics of life: one molecule at a time." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1611 (February 5, 2013): 20120248. http://dx.doi.org/10.1098/rstb.2012.0248.

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The esteemed physicist Erwin Schrödinger, whose name is associated with the most notorious equation of quantum mechanics, also wrote a brief essay entitled ‘What is Life?’, asking: ‘How can the events in space and time which take place within the spatial boundary of a living organism be accounted for by physics and chemistry?’ The 60+ years following this seminal work have seen enormous developments in our understanding of biology on the molecular scale, with physics playing a key role in solving many central problems through the development and application of new physical science techniques, biophysical analysis and rigorous intellectual insight. The early days of single-molecule biophysics research was centred around molecular motors and biopolymers, largely divorced from a real physiological context. The new generation of single-molecule bioscience investigations has much greater scope, involving robust methods for understanding molecular-level details of the most fundamental biological processes in far more realistic, and technically challenging, physiological contexts, emerging into a new field of ‘single-molecule cellular biophysics’. Here, I outline how this new field has evolved, discuss the key active areas of current research and speculate on where this may all lead in the near future.

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4

Connelly, Patrick R. "Recent drug discovery success signals renaissance in biophysics." Biophysics Reviews 3, no. 2 (June 2022): 020401. http://dx.doi.org/10.1063/5.0099305.

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With a scope that spans the hierarchy of biological organization from molecules and cells to organisms and populations, the discipline of biophysics has been proven to be particularly well suited for connecting the molecular embodiments of human diseases to the medical conditions experienced by patients. Recently, fundamental biophysical research on aberrant proteins involved in maintaining salt and water balance in our lungs, oxygen transport from our lungs to the rest of the body, and the pumping of blood by our hearts have been successfully translated to the creation of transformational new medicines that are radically changing the lives of patients. With these and other emerging discoveries, the field of applied biophysics is experiencing the beginnings of a veritable renaissance era.

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5

Kopūstas, Aurimas, Mindaugas Zaremba, and Marijonas Tutkus. "DNA Flow-Stretch Assays for Studies of Protein-DNA Interactions at the Single-Molecule Level." Applied Nano 3, no. 1 (January 11, 2022): 16–41. http://dx.doi.org/10.3390/applnano3010002.

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Protein-DNA interactions are the core of the cell’s molecular machinery. For a long time, conventional biochemical methods served as a powerful investigatory basis of protein-DNA interactions and target search mechanisms. Currently single-molecule (SM) techniques have emerged as a complementary tool for studying these interactions and have revealed plenty of previously obscured mechanistic details. In comparison to the traditional ones, SM methods allow direct monitoring of individual biomolecules. Therefore, SM methods reveal reactions that are otherwise hidden by the ensemble averaging observed in conventional bulk-type methods. SM biophysical techniques employing various nanobiotechnology methods for immobilization of studied molecules grant the possibility to monitor individual reaction trajectories of biomolecules. Next-generation in vitro SM biophysics approaches enabling high-throughput studies are characterized by much greater complexity than the ones developed previously. Currently, several high-throughput DNA flow-stretch assays have been published and have shown many benefits for mechanistic target search studies of various DNA-binding proteins, such as CRISPR-Cas, Argonaute, various ATP-fueled helicases and translocases, and others. This review focuses on SM techniques employing surface-immobilized and relatively long DNA molecules for studying protein-DNA interaction mechanisms.

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6

Alishahi, Marzieh, and Reza Kamali. "Forced diffusion of water molecules through aquaporin-5 biomembrane; a molecular dynamics study." Biophysics and Physicobiology 15 (2018): 255–62. http://dx.doi.org/10.2142/biophysico.15.0_255.

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7

Furlan, Aurélien L., Yoann Laurin, Camille Botcazon, Nely Rodríguez-Moraga, Sonia Rippa, Magali Deleu, Laurence Lins, Catherine Sarazin, and Sébastien Buchoux. "Contributions and Limitations of Biophysical Approaches to Study of the Interactions between Amphiphilic Molecules and the Plant Plasma Membrane." Plants 9, no. 5 (May 20, 2020): 648. http://dx.doi.org/10.3390/plants9050648.

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Some amphiphilic molecules are able to interact with the lipid matrix of plant plasma membranes and trigger the immune response in plants. This original mode of perception is not yet fully understood and biophysical approaches could help to obtain molecular insights. In this review, we focus on such membrane-interacting molecules, and present biophysically grounded methods that are used and are particularly interesting in the investigation of this mode of perception. Rather than going into overly technical details, the aim of this review was to provide to readers with a plant biochemistry background a good overview of how biophysics can help to study molecular interactions between bioactive amphiphilic molecules and plant lipid membranes. In particular, we present the biomimetic membrane models typically used, solid-state nuclear magnetic resonance, molecular modeling, and fluorescence approaches, because they are especially suitable for this field of research. For each technique, we provide a brief description, a few case studies, and the inherent limitations, so non-specialists can gain a good grasp on how they could extend their toolbox and/or could apply new techniques to study amphiphilic bioactive compound and lipid interactions.

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8

Sikosek, Tobias, and Hue Sun Chan. "Biophysics of protein evolution and evolutionary protein biophysics." Journal of The Royal Society Interface 11, no. 100 (November 6, 2014): 20140419. http://dx.doi.org/10.1098/rsif.2014.0419.

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The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution.

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9

Deniz, Ashok A., Samrat Mukhopadhyay, and Edward A. Lemke. "Single-molecule biophysics: at the interface of biology, physics and chemistry." Journal of The Royal Society Interface 5, no. 18 (May 22, 2007): 15–45. http://dx.doi.org/10.1098/rsif.2007.1021.

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Single-molecule methods have matured into powerful and popular tools to probe the complex behaviour of biological molecules, due to their unique abilities to probe molecular structure, dynamics and function, unhindered by the averaging inherent in ensemble experiments. This review presents an overview of the burgeoning field of single-molecule biophysics, discussing key highlights and selected examples from its genesis to our projections for its future. Following brief introductions to a few popular single-molecule fluorescence and manipulation methods, we discuss novel insights gained from single-molecule studies in key biological areas ranging from biological folding to experiments performed in vivo .

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10

Zhang, Yujia, Jessica Bates, Benoit Gourdet, Louise Birch, Philip Addis, Roland Hjerpe, and Allan M. Jordan. "Abstract 3429: Beyond cereblon IMIDs - biophysics-based discovery of novel molecular glue chemotypes." Cancer Research 83, no. 7_Supplement (April 4, 2023): 3429. http://dx.doi.org/10.1158/1538-7445.am2023-3429.

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Abstract Molecular glue degraders are compact, low molecular weight molecules that can efficiently induce specific and potent degradation of a target protein. This class of degraders function by inducing interactions between a target of interest and a ubiquitin-ligase, either by stabilization of weak pre-existing interactions, or by generation of entirely novel interactions. These molecules offer significant opportunity beyond heterobifunctional degraders such as PROTACs, not least in terms of improved molecular properties. However, beyond the IMID molecular glues, typified by thalidomide, pomalidomide and lenalidomide, novel molecular glue chemotypes remain scarce. To address this need, we have developed biophysics-based molecular glue screening platform, exploiting our internal, high quality fragment library and proximity-based screening platforms to rapidly identify promising new molecular glues for further optimization. A potential advantage of utilizing cell-free biophysical systems is the opportunity to select both the target and the desired ligase, opening up for development of degraders that capitalize upon differential expression of ligases in different tissues. As proof of concept, we have applied this platform to find new molecular glues to degrade CK1α. This Ser/Thr kinase has been found to be over-expressed in metastatic colorectal cancer, and this over-expression correlates with poor overall survival. The kinase has also been implicated as an oncogenic driver in tumors such as B-Cell lymphomas and non-Hodgkin lymphomas, suggesting a potential therapeutic application for novel CK1α molecular glues. Utilizing known IMID-derived molecular glues between CK1α and CRBN as benchmark controls, we identified several non-IMID derived chemotypes as tentative stabilizers of the CRBN/CK1α interaction. Further studies on these novel candidate degrader templates are now underway. Citation Format: Yujia Zhang, Jessica Bates, Benoit Gourdet, Louise Birch, Philip Addis, Roland Hjerpe, Allan M. Jordan. Beyond cereblon IMIDs - biophysics-based discovery of novel molecular glue chemotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3429.

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11

Sloan, Phillip R. "Molecularizing Chicago—1945–1965." Historical Studies in the Natural Sciences 44, no. 4 (November 2012): 364–412. http://dx.doi.org/10.1525/hsns.2014.44.4.364.

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This paper examines the history of biophysics at the University of Chicago, with a specific focus on the history of the Institute for Radiobiology and Biophysics (IRB), established at the university in 1945 as a continuation of the Manhattan Project. Discussed herein is how biophysical research developed at Chicago, and how the IRB formed the locus for early work in photosynthesis, phage genetics, and nucleic acid chemistry. The discontinuation of this institution in 1954 did not, however, terminate such work, but led to its dispersal into other entities within the university. Therefore the dramatic institutionalization of “molecular biology” and the creation of the Department of Biophysics under the presidency of George Beadle that commenced in the early 1960s relied upon a preexisting tradition rather than creating a new molecular phase in Chicago biology. This paper also shows that the interest in topics such as phage genetics and nucleic acid chemistry were continuous developments at Chicago from the early 1950s and did not represent a late interest in these topics.

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12

Rieth, Monica D. "Instructional Design for an Undergraduate Laboratory Course in Molecular Biophysics." Biophysicist 2, no. 3 (December 1, 2021): 41–54. http://dx.doi.org/10.35459/tbp.2020.000173.

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ABSTRACT In this article, an approach to teaching molecular biophysics is described. The organization and course content has been carefully chosen and curated so that fundamental ideas in molecular biophysics can be taught effectively to upper classmen in higher education. Three general topic areas are introduced along with accompanying experiments that illustrate major principles related to each topic area. This article outlines an approach to organizing chosen course material and suggests multiple teaching activities within each major topic area: thermodynamics, kinetics, and structural biology. Subtopics are presented along with suggested laboratory experiments. The experiments are outlined in a way that they can be readily adopted by educators teaching a biophysical chemistry lab. The accompaniment of workshop exercises as an additional teaching modality is a component of the course intended to enhance the development of important problem-solving skills and comprehension of new content. Finally, a reflection on student feedback and course outcomes along with targeted learning goals is discussed.

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13

Toyabe, Shoichi, and Eiro Muneyuki. "Experimental thermodynamics of single molecular motor." BIOPHYSICS 9 (2013): 91–98. http://dx.doi.org/10.2142/biophysics.9.91.

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14

Gilliard, Guillaume, Aurélien L. Furlan, Willy Smeralda, Jelena Pršić, and Magali Deleu. "Added Value of Biophysics to Study Lipid-Driven Biological Processes: The Case of Surfactins, a Class of Natural Amphiphile Molecules." International Journal of Molecular Sciences 23, no. 22 (November 10, 2022): 13831. http://dx.doi.org/10.3390/ijms232213831.

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The role of membrane lipids is increasingly claimed to explain biological activities of natural amphiphile molecules. To decipher this role, biophysical studies with biomimetic membrane models are often helpful to obtain insights at the molecular and atomic levels. In this review, the added value of biophysics to study lipid-driven biological processes is illustrated using the case of surfactins, a class of natural lipopeptides produced by Bacillus sp. showing a broad range of biological activities. The mechanism of interaction of surfactins with biomimetic models showed to be dependent on the surfactins-to-lipid ratio with action as membrane disturber without membrane lysis at low and intermediate ratios and a membrane permeabilizing effect at higher ratios. These two mechanisms are relevant to explain surfactins’ biological activities occurring without membrane lysis, such as their antiviral and plant immunity-eliciting activities, and the one involving cell lysis, such as their antibacterial and hemolytic activities. In both biological and biophysical studies, influence of surfactin structure and membrane lipids on the mechanisms was observed with a similar trend. Hence, biomimetic models represent interesting tools to elucidate the biological mechanisms targeting membrane lipids and can contribute to the development of new molecules for pharmaceutical or agronomic applications.

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15

Hall, Damien. "Biophysical Reviews—the IUPAB journal tasked with advancing biophysics." Biophysical Reviews 13, no. 1 (February 2021): 1–6. http://dx.doi.org/10.1007/s12551-021-00788-8.

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16

Ando, Toshio. "Biophysical reviews top five: atomic force microscopy in biophysics." Biophysical Reviews 13, no. 4 (July 10, 2021): 455–58. http://dx.doi.org/10.1007/s12551-021-00820-x.

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AbstractSince its invention in the late 1980s, atomic force microscopy (AFM), in which a nanometer-sized tip is used to physically interrogate the properties of a surface at high resolution, has brought about scientific revolutions in both surface science and biological physics. In response to a request from the journal, I have prepared a top-five list of scientific papers that I feel represent truly landmark developments in the use of AFM in the biophysics field. This selection is necessarily limited by number (just five) and subjective (my opinion) and I offer my apologies to those not appearing in this list.

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17

Kinz-Thompson, Colin D., Korak Kumar Ray, and Ruben L. Gonzalez. "Bayesian Inference: The Comprehensive Approach to Analyzing Single-Molecule Experiments." Annual Review of Biophysics 50, no. 1 (May 6, 2021): 191–208. http://dx.doi.org/10.1146/annurev-biophys-082120-103921.

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Biophysics experiments performed at single-molecule resolution provide exceptional insight into the structural details and dynamic behavior of biological systems. However, extracting this information from the corresponding experimental data unequivocally requires applying a biophysical model. In this review, we discuss how to use probability theory to apply these models to single-molecule data. Many current single-molecule data analysis methods apply parts of probability theory, sometimes unknowingly, and thus miss out on the full set of benefits provided by this self-consistent framework. The full application of probability theory involves a process called Bayesian inference that fully accounts for the uncertainties inherent to single-molecule experiments. Additionally, using Bayesian inference provides a scientifically rigorous method of incorporating information from multiple experiments into a single analysis and finding the best biophysical model for an experiment without the risk of overfitting the data. These benefits make the Bayesian approach ideal for analyzing any type of single-molecule experiment.

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18

Pohl, Peter. "Biophysical Reviews’ “Meet the Councilor Series”—a profile of Peter Pohl." Biophysical Reviews 13, no. 6 (November 23, 2021): 839–44. http://dx.doi.org/10.1007/s12551-021-00897-4.

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AbstractIt is my pleasure to write a few words to introduce myself to the readers of Biophysical Reviews as part of the “Meet the Councilor Series.” Currently, I am serving the second period as IUPAB councilor after having been elected first in 2017. Initially, I studied Biophysics in Moscow (Russia) and later Medicine in Halle (Germany). My scientific carrier took me from the Medical School of the Martin Luther University of Halle-Wittenberg, via the Leibniz Institute for Molecular Pharmacology (Berlin) and the Institute for Biology at the Humboldt University (Berlin) to the Physics Department of the Johannes Kepler University in Linz (Austria). My key research interests lie in the molecular mechanisms of transport phenomena occurring at the lipid membrane, including (i) spontaneous and facilitated transport of water and other small molecules across membranes in reconstituted systems, (ii) proton migration along the membrane surface, (iii) protein translocation, and (iv) bilayer mechanics. Training of undergraduate, graduate, and postdoctoral researchers from diverse academic disciplines has been—and shall remain—a consistent part of my work.

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19

Li, Juan, Qing Wang, Huiling Liang, Haoxu Dong, Yan Li, Ernest Hung Yu Ng, and Xiaoke Wu. "Biophysical Characteristics of Meridians and Acupoints: A Systematic Review." Evidence-Based Complementary and Alternative Medicine 2012 (2012): 1–6. http://dx.doi.org/10.1155/2012/793841.

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As an integral part of traditional Chinese medicine (TCM), acupuncture is a convenient and effective therapy with fewer adverse effects. Recently, researches on meridian essence have become core issues of modern TCM. Numerous experiments have demonstrated the objective existence of meridians by different technologies since 1950s, such as biophysics, biochemistry, and molecular biology. In this paper, we review biophysical studies on electric, acoustic, thermal, optical, magnetic, isotopic, and myoelectric aspects of meridians and acupoints. These studies suggest that meridians/acupoints have biophysical characteristics which are different from nonacupuncture points. Owing to the limitations of previous studies, future research using high-throughput technologies such as omics and multicenter randomized controlled trials should be performed to explore the acupuncture’s mechanisms of action and demonstration of efficacy.

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20

Ishiwata, Shin'ichi. "1SA54 Biophysics of Molecular Motors("Japan-Australia Joint Symposium on Biophysics" (English Session))." Seibutsu Butsuri 45, supplement (2005): S2. http://dx.doi.org/10.2142/biophys.45.s2_1.

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21

Taniguchi, Yukinori, Akiko Kobayashi, and Masaru Kawakami. "Mechanical unfolding studies of protein molecules." BIOPHYSICS 8 (2012): 51–58. http://dx.doi.org/10.2142/biophysics.8.51.

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22

Nakamura, Haruki. "Announcing changes to the publishing procedures of “Biophysics and Physicobiology” (BPPB)—the Biophysical Society of Japan’s English language biophysics journal." Biophysical Reviews 13, no. 6 (November 16, 2021): 813–14. http://dx.doi.org/10.1007/s12551-021-00882-x.

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AbstractThis Commentary describes some upcoming changes to the submission and payment procedures to the Biophysical Society of Japan’s English language journal “Biophysics and Physicobiology” (BPPB) that will facilitate a much easier and cheaper publishing experience for all scientists—whether they be Japan-based or located internationally.

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23

Ando, Nozomi, Blanca Barquera, Douglas H. Bartlett, Eric Boyd, Audrey A. Burnim, Amanda S. Byer, Daniel Colman, et al. "The Molecular Basis for Life in Extreme Environments." Annual Review of Biophysics 50, no. 1 (May 6, 2021): 343–72. http://dx.doi.org/10.1146/annurev-biophys-100120-072804.

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Sampling and genomic efforts over the past decade have revealed an enormous quantity and diversity of life in Earth's extreme environments. This new knowledge of life on Earth poses the challenge of understandingits molecular basis in such inhospitable conditions, given that such conditions lead to loss of structure and of function in biomolecules from mesophiles. In this review, we discuss the physicochemical properties of extreme environments. We present the state of recent progress in extreme environmental genomics. We then present an overview of our current understanding of the biomolecular adaptation to extreme conditions. As our current and future understanding of biomolecular structure–function relationships in extremophiles requires methodologies adapted to extremes of pressure, temperature, and chemical composition, advances in instrumentation for probing biophysical properties under extreme conditions are presented. Finally, we briefly discuss possible future directions in extreme biophysics.

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24

Nishikata, Koro, Sotaro Fuchigami, Mitsunori Ikeguchi, and Akinori Kidera. "Molecular modeling of the HAMP domain of sensory rhodopsin II transducer from Natronomonas pharaonis." BIOPHYSICS 6 (2010): 27–36. http://dx.doi.org/10.2142/biophysics.6.27.

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25

Tang, Qian, and Da Han. "Obtaining Precise Molecular Information via DNA Nanotechnology." Membranes 11, no. 9 (September 2, 2021): 683. http://dx.doi.org/10.3390/membranes11090683.

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Precise characterization of biomolecular information such as molecular structures or intermolecular interactions provides essential mechanistic insights into the understanding of biochemical processes. As the resolution of imaging-based measurement techniques improves, so does the quantity of molecular information obtained using these methodologies. DNA (deoxyribonucleic acid) molecule have been used to build a variety of structures and dynamic devices on the nanoscale over the past 20 years, which has provided an accessible platform to manipulate molecules and resolve molecular information with unprecedented precision. In this review, we summarize recent progress related to obtaining precise molecular information using DNA nanotechnology. After a brief introduction to the development and features of structural and dynamic DNA nanotechnology, we outline some of the promising applications of DNA nanotechnology in structural biochemistry and in molecular biophysics. In particular, we highlight the use of DNA nanotechnology in determination of protein structures, protein–protein interactions, and molecular force.

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26

Watanabe, Hiroshi C., Yoshiharu Mori, Takashi Tada, Shozo Yokoyama, and Takahisa Yamato. "Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin." BIOPHYSICS 6 (2010): 67–78. http://dx.doi.org/10.2142/biophysics.6.67.

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27

Hall, Damien. "Biophysical Reviews: a Q1 ranked journal in biophysics and structural biology." Biophysical Reviews 12, no. 5 (September 29, 2020): 1085–89. http://dx.doi.org/10.1007/s12551-020-00764-8.

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28

Yavuz, Mehmet, and Fuat Usta. "Importance of modelling and simulation in biophysical applications." AIMS Biophysics 10, no. 3 (2023): 258–62. http://dx.doi.org/10.3934/biophy.2023017.

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<abstract> <p>Mathematical modelling and simulation in biophysics and its applications in terms of both theoretical and biological/physical/ecological point of view arise in a number of research problems ranging from physical and chemical processes to biomathematics and life science. As known, the modeling of a biophysical system requires the analysis of the different interactions occurring among the different components of the system. This editorial article deals with the topic of this special issue, which is devoted to the new developments in the modelling and simulation in biophysical applications with special attention to the interplay between different scholars.</p> </abstract>

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29

Kinoshita, Masanao, and Satoru Kato. "Intermolecular interaction of phosphatidylinositol with the lipid raft molecules sphingomyelin and cholesterol." BIOPHYSICS 4 (2008): 1–9. http://dx.doi.org/10.2142/biophysics.4.1.

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30

L. Harris, Andrew. "Emerging issues of connexin channels: biophysics fills the gap." Quarterly Reviews of Biophysics 34, no. 3 (August 2001): 325–472. http://dx.doi.org/10.1017/s0033583501003705.

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1. Introduction 3261.1 What? Terminology and general properties 3271.2 Why? Reasons for biophysical study 3291.3 How? Special issues for study of connexin channels 3302. Molecular and structural context 3312.1 Biochemical features 3312.2 Structures 3342.2.1 Junctional channels 3352.2.2 Hemichannels 3382.2.3 Heteromeric channels 3422.2.4 Junctional plaques 3473. Experimental approaches and issues specific to study of connexin channel physiology 3493.1 Macroscopic currents 3493.1.1 Junctional channels 3493.1.2 Hemichannels 3543.2 Single-channel currents 3553.2.1 Junctional channels 3553.2.2 Hemichannels 3583.3 Molecular permeability 3613.3.1 A selection of tracers 3613.3.2 Junctional channels 3623.3.3 Hemichannels 3663.4 Other 3674. Structural issues 3684.1 What lines the pore? 3684.2 Docking between hemichannels 3734.2.1 Structural and molecular basis 3744.2.2 Determinants of specificity of interaction 3805. Permeability and selectivity 3815.1 Among the usual ions 3835.1.1 Unitary conductance 3835.1.2 Selectivity 3845.1.3 Nonlinear single-channel I–V relations and their molecular determinants 3865.2 Among large permeants 3915.2.1 Uncharged molecules 3925.2.2 Charged molecules 3935.2.3 Cytoplasmic/signaling molecules 3966. Voltage sensitivity 3996.1 Macroscopic transjunctional voltage sensitivity 4046.2 Microscopic voltage sensitivity – Vj-gating 4076.2.1 Molecular basis – voltage sensor 4076.2.2 Molecular basis – transduction and/or state stability 4096.3 Microscopic voltage sensitivity – loop gating 4126.4 Vm-gating 4147. Direct chemical modulation 4157.1 Phosphorylation 4177.2 Cytoplasmic pH and aminosulfonates 4197.3 Calcium ion 4247.4 Lipophiles 4247.4.1 Long chain n-alkyl alcohols 4257.4.2 Fatty acids and fatty acid amides 4267.4.3 Halothane 4267.5 Glycyrrhetinic acid and derivatives 4277.6 Cyclic nucleotides 4287.7 Other candidates 4308. Connexinopathies 4319. Summary 43510. Acknowledgements 43811. References 438Connexins are the proteins that form the intercellular channels that compose gap junctions in vertebrates. Connexin channels mediate electrotonic coupling between cells and serve important functions as mediators of intercellular molecular signaling. Convincing demonstration of the latter function has been elusive, as have the experimental tools required for detailed functional study of the channels. Recently, substantial progress has been made on both fronts. Connexin channels are now known to be dynamic, multifunctional channels intimately involved in development, physiology and pathology, and amenable to study by state-of-the-art approaches. A host of developmental and physiological defects are caused by defects in connexin channels, and therefore in the intercellular molecular movement they mediate. The channel structure has been determined to 7·5 Å resolution within the plane of the membrane. Experimental paradigms have been developed that enable application of the tools of modern channel biophysics to study connexin channel structure–function. As a result, the biophysical mechanisms and biological functions of connexin channels now enjoy a vigorous and expanding experimental interest. This article focuses on the former, but with attention to issues likely to have biological consequences.

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31

Nossal, Ralph J., Harold Lecar, and David Kleinfeld. "Molecular and Cell Biophysics." Physics Today 45, no. 5 (May 1992): 62–63. http://dx.doi.org/10.1063/1.2809665.

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32

Brenner, Michael P., and Pia M. Sörensen. "Biophysics of Molecular Gastronomy." Cell 161, no. 1 (March 2015): 5–8. http://dx.doi.org/10.1016/j.cell.2015.03.002.

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33

Sakano, Takako, Md Iqbal Mahamood, Takefumi Yamashita, and Hideaki Fujitani. "Molecular dynamics analysis to evaluate docking pose prediction." Biophysics and Physicobiology 13 (2016): 181–94. http://dx.doi.org/10.2142/biophysico.13.0_181.

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Goñi, Félix M., F.-Xabier Contreras, L.-Ruth Montes, Jesús Sot, and Alicia Alonso. "Biophysics (and sociology) of ceramides." Biochemical Society Symposia 72 (January 1, 2005): 177–88. http://dx.doi.org/10.1042/bss0720177.

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In the past decade, the long-neglected ceramides (N-acylsphingosines) have become one of the most attractive lipid molecules in molecular cell biology, because of their involvement in essential structures (stratum corneum) and processes (cell signalling). Most natural ceramides have a long (16-24 C atoms) N-acyl chain, but short N-acyl chain ceramides (two to six C atoms) also exist in Nature, apart from being extensively used in experimentation, because they can be dispersed easily in water. Long-chain ceramides are among the most hydrophobic molecules in Nature, they are totally insoluble in water and they hardly mix with phospholipids in membranes, giving rise to ceramide-enriched domains. In situ enzymic generation, or external addition, of long-chain ceramides in membranes has at least three important effects: (i) the lipid monolayer tendency to adopt a negative curvature, e.g. through a transition to an inverted hexagonal structure, is increased, (ii) bilayer permeability to aqueous solutes is notoriously enhanced, and (iii) transbilayer (flip-flop) lipid motion is promoted. Short-chain ceramides mix much better with phospholipids, promote a positive curvature in lipid monolayers, and their capacities to increase bilayer permeability or transbilayer motion are very low or non-existent.

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35

Raviv, Uri. "1SQ-03 Structure and Intermolecular interactions of bio-molecular self-assemblies(1SQ Israel-Japan Joint Symposium on Biophysics "Protein Dynamics: From single molecules to whole cell",The 49th Annual Meeting of the Biophysical Society of Japan)." Seibutsu Butsuri 51, supplement (2011): S13. http://dx.doi.org/10.2142/biophys.51.s13_1.

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36

Strange, Kevin, Toshiki Yamada, and Jerod S. Denton. "A 30-year journey from volume-regulated anion currents to molecular structure of the LRRC8 channel." Journal of General Physiology 151, no. 2 (January 16, 2019): 100–117. http://dx.doi.org/10.1085/jgp.201812138.

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The swelling-activated anion channel VRAC has fascinated and frustrated physiologists since it was first described in 1988. Multiple laboratories have defined VRAC’s biophysical properties and have shown that it plays a central role in cell volume regulation and possibly other fundamental physiological processes. However, confusion and intense controversy surrounding the channel’s molecular identity greatly hindered progress in the field for >15 yr. A major breakthrough came in 2014 with the demonstration that VRAC is a heteromeric channel encoded by five members of the Lrrc8 gene family, Lrrc8A–E. A mere 4 yr later, four laboratories described cryo-EM structures of LRRC8A homomeric channels. As the melee of structure/function and physiology studies begins, it is critical that this work be framed by a clear understanding of VRAC biophysics, regulation, and cellular physiology as well as by the field’s past confusion and controversies. That understanding is essential for the design and interpretation of structure/function studies, studies of VRAC physiology, and studies aimed at addressing the vexing problem of how the channel detects cell volume changes. In this review we discuss key aspects of VRAC biophysics, regulation, and function and integrate these into our emerging understanding of LRRC8 protein structure/function.

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37

Tanaka, Wataru, Mitsuo Shoji, Fumiaki Tomoike, Yuzuru Ujiie, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, et al. "Molecular mechanisms of substrate specificities of uridine-cytidine kinase." Biophysics and Physicobiology 13 (2016): 77–84. http://dx.doi.org/10.2142/biophysico.13.0_77.

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Inoue, Yasuhiro, Satoru Okuda, Tetsuya Fujii, Kohei Ohto, and Taiji Adachi. "2SEA-04 Computational biophysics on epithelial tissue deformation : from molecular to tissue scale(2SEA Biophysical views in structural cell biology,Symposium,The 51th Annual Meeting of the Biophysical Society of Japan)." Seibutsu Butsuri 53, supplement1-2 (2013): S96. http://dx.doi.org/10.2142/biophys.53.s96_1.

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39

Li, Qingxin, and CongBao Kang. "Mechanisms of Action for Small Molecules Revealed by Structural Biology in Drug Discovery." International Journal of Molecular Sciences 21, no. 15 (July 24, 2020): 5262. http://dx.doi.org/10.3390/ijms21155262.

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Small-molecule drugs are organic compounds affecting molecular pathways by targeting important proteins. These compounds have a low molecular weight, making them penetrate cells easily. Small-molecule drugs can be developed from leads derived from rational drug design or isolated from natural resources. A target-based drug discovery project usually includes target identification, target validation, hit identification, hit to lead and lead optimization. Understanding molecular interactions between small molecules and their targets is critical in drug discovery. Although many biophysical and biochemical methods are able to elucidate molecular interactions of small molecules with their targets, structural biology is the most powerful tool to determine the mechanisms of action for both targets and the developed compounds. Herein, we reviewed the application of structural biology to investigate binding modes of orthosteric and allosteric inhibitors. It is exemplified that structural biology provides a clear view of the binding modes of protease inhibitors and phosphatase inhibitors. We also demonstrate that structural biology provides insights into the function of a target and identifies a druggable site for rational drug design.

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40

Nakashima, Hitomi, Chika Okimura, and Yoshiaki Iwadate. "The molecular dynamics of crawling migration in microtubule-disrupted keratocytes." Biophysics and Physicobiology 12 (2015): 21–29. http://dx.doi.org/10.2142/biophysico.12.0_21.

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41

Hashimoto, Hiroshi, Asami Hishiki, Kodai Hara, and Sotaro Kikuchi. "Structural basis for the molecular interactions in DNA damage tolerances." Biophysics and Physicobiology 14 (2017): 199–205. http://dx.doi.org/10.2142/biophysico.14.0_199.

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42

Das, Sumita, Tomoki P. Terada, and Masaki Sasai. "Single-molecular and ensemble-level oscillations of cyanobacterial circadian clock." Biophysics and Physicobiology 15 (2018): 136–50. http://dx.doi.org/10.2142/biophysico.15.0_136.

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43

Bardhan, Jaydeep P. "Gradient models in molecular biophysics: progress, challenges, opportunities." Journal of the Mechanical Behavior of Materials 22, no. 5-6 (December 1, 2013): 169–84. http://dx.doi.org/10.1515/jmbm-2013-0024.

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AbstractIn the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g., molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding nonlocal dielectric response. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain, and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost 40 years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The review concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics.

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44

Riznichenk, Galina, Ilya Kovalenko, Vladimir Fedorov, Sergei Khruschev, and Andrey Rubin. "Photosynthetic Electron Transfer by Dint of Protein Mobile Carriers. Multi-particle Brownian and Molecular Modeling." EPJ Web of Conferences 224 (2019): 03008. http://dx.doi.org/10.1051/epjconf/201922403008.

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The paper presents the review of works on modeling the interaction of photosynthetic proteins using the multiparticle Brownian dynamics method developed at the Department of Biophysics, Biological Faculty, Lomonosov Moscow State University. The method describes the displacement of individual macromolecules – mobile electron carriers, and their electrostatic interactions between each other and with pigment-protein complexes embedded in photosynthetic membrane. Three-dimensional models of the protein molecules were constructed on the basis of the data from the Protein Data Bank. We applied the Brownian methods coupled to molecular dynamic simulations to reveal the role of electrostatic interactions and conformational motions in the transfer of an electron from the cytochrome complex Cyt b6f) membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and to the molecule of the mobile carrier plastocyanin (Pc) in plants, green algae and cyanic bacteria. Taking into account the interior of photosynthetic membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and Cyt b6f, embedded in photosynthetic membrane, electron transfer and complex dissociation. Multiparticle Brownian simulation method can be used to consider the processes of protein interactions in subcellular systems in order to clarify the role of individual stages and the biophysical mechanisms of these processes.

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45

Luo, Shuqi, Samuel Wohl, Wenwei Zheng, and Sichun Yang. "Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery." Biomolecules 13, no. 3 (March 14, 2023): 530. http://dx.doi.org/10.3390/biom13030530.

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Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and computational methods and further describe integrative strategies available for combining these techniques. Integrative biophysics methods provide valuable insights into the sequence–structure–function relationship of disordered proteins, setting the stage for protein intrinsic disorder to become a promising target for drug discovery. Finally, we briefly summarize recent advances in the development of new small molecule inhibitors targeting the disordered N-terminal domains of three vital transcription factors.

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46

Leake, Mark C., and Steven D. Quinn. "A guide to small fluorescent probes for single-molecule biophysics." Chemical Physics Reviews 4, no. 1 (March 2023): 011302. http://dx.doi.org/10.1063/5.0131663.

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The explosive growth of single-molecule techniques is transforming our understanding of biology, helping to develop new physics inspired by emergent biological processes, and leading to emerging areas of nanotechnology. Key biological and chemical processes can now be probed with new levels of detail, one molecule at a time, from the nanoscopic dynamics of nature's molecular machines to an ever-expanding range of exciting applications across multiple length and time scales. Their common feature is an ability to render the underlying distribution of molecular properties that ensemble averaging masks and to reveal new insights into complex systems containing spatial and temporal heterogeneity. Small fluorescent probes are among the most adaptable and versatile for single-molecule sensing applications because they provide high signal-to-noise ratios combined with excellent specificity of labeling when chemically attached to target biomolecules or embedded within a host material. In this review, we examine recent advances in probe designs, their utility, and applications and provide a practical guide to their use, focusing on the single-molecule detection of nucleic acids, proteins, carbohydrates, and membrane dynamics. We also present key challenges that must be overcome to perform successful single-molecule experiments, including probe conjugation strategies, identify tradeoffs and limitations for each probe design, showcase emerging applications, and discuss exciting future directions for the community.

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47

Noji, Hroyuki. "SINGLE MOLECULE BIOPHYSICS OF F_1-ATPase motor protein." Proceedings of the Asian Pacific Conference on Biomechanics : emerging science and technology in biomechanics 2007.3 (2007): S1. http://dx.doi.org/10.1299/jsmeapbio.2007.3.s1.

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48

Takano, Yu, Ayumi Kusaka, and Haruki Nakamura. "Density functional study of molecular interactions in secondary structures of proteins." Biophysics and Physicobiology 13 (2016): 27–35. http://dx.doi.org/10.2142/biophysico.13.0_27.

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49

Yamauchi, Yumeka, Masae Konno, Shota Ito, Satoshi P. Tsunoda, Keiichi Inoue, and Hideki Kandori. "Molecular properties of a DTD channelrhodopsin from Guillardia theta." Biophysics and Physicobiology 14 (2017): 57–66. http://dx.doi.org/10.2142/biophysico.14.0_57.

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50

Serdyuk, I. N., and E. I. Deryusheva. "Biophysics of single molecules." Biophysics 56, no. 5 (October 2011): 858–82. http://dx.doi.org/10.1134/s0006350911050186.

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