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Journal articles on the topic 'Biophysical Investigations'

Author: Grafiati

Published: 6 September 2023

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1

Becker, R., J. Bienen, U. Carl, P. Cloth, M. Dellert, V. Dr ke, W. Eyrich, et al. "Biophysical Investigations of Therapeutic Proton Beams." Radiation Protection Dosimetry 70, no. 1 (April 1, 1997): 485–92. http://dx.doi.org/10.1093/oxfordjournals.rpd.a032002.

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2

Hosur, R. V., P. K. Radha, Anup Madan, and L. C. Padhy. "Biophysical investigations on the myb-DNA system." Biophysical Chemistry 68, no. 1-3 (October 1997): 147–59. http://dx.doi.org/10.1016/s0301-4622(97)00026-4.

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3

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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4

Rounsevell, Ross W. S., Annette Steward, and Jane Clarke. "Biophysical Investigations of Engineered Polyproteins: Implications for Force Data." Biophysical Journal 88, no. 3 (March 2005): 2022–29. http://dx.doi.org/10.1529/biophysj.104.053744.

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5

Brandenburg, K., I. Moriyon, M. D. Arraiza, G. Lewark-Yvetot, M. H. J. Koch, and U. Seydel. "Biophysical investigations into the interaction of lipopolysaccharide with polymyxins." Thermochimica Acta 382, no. 1-2 (January 2002): 189–98. http://dx.doi.org/10.1016/s0040-6031(01)00731-6.

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6

Kenkare, U. W., G. K. Jarori, S. R. Kasturi, A. Mehta, and M. P. Pitale. "Biophysical investigations on the active site of brain hexokinase." Journal of Biosciences 8, no. 1-2 (August 1985): 107–19. http://dx.doi.org/10.1007/bf02703970.

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7

De, Kathakali, Christopher Aisenbrey, Jayanta Haldar, Sophie Faure, Christiane Forestier, Nicolas Charbonnel, and Burkhard Bechinger. "Biophysical investigations of antimicrobial peptide mimics for mechanistic studies." Biophysical Journal 122, no. 3 (February 2023): 368a. http://dx.doi.org/10.1016/j.bpj.2022.11.2030.

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8

Chen, F., X. W. Shen, D. F. Huang, and Y. X. Huang. "THERMAL ENVIRONMENT OF RESIDENTIAL COMMUNITIES OVER A COAST AREA IN SOUTHEASTERN CHINA." International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLVIII-3/W2-2022 (October 27, 2022): 9–14. http://dx.doi.org/10.5194/isprs-archives-xlviii-3-w2-2022-9-2022.

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Abstract. The characters of the residential communities over Tong’an District of Xiamen City in thermal environment as well as in biophysical factors were investigated mainly based on the Lansat-8 OLI/TIRS Collection 2 Level-2 products. Specifically, the surface temperature product was used in measuring thermal environment, and the surface reflectance product was used to derive biophysical factors through the tasseled cap transformation as well as the normalized difference vegetation index (NDVI). Among the four types of residential community, the old community in urban area was generally lower in NDVI and in the Wetness component and therefore had higher surface temperature. Varied relationships of surface temperature with biophysical factors among four types were observed, which also demonstrated seasonal variation. At the same time, the preliminary investigation showed that the residential communities located in rural-urban fringe and a small portion of village communities had confronted with problems in thermal environment as well as in surface biophysical conditions. Furthermore, limitations of this study were discussed, mainly in spatial resolution and temporal representativeness of the Landsat-8 OLI/TIRS data, in biophysical components derived from the multi-spectral reflectance without depicting actual landscape, and in no consideration for the background of individual community. As the whole district covers wide and complex territory along with different local climate types, more investigations in details are required.

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9

Plotegher, Nicoletta, Elisa Greggio, Marco Bisaglia, and Luigi Bubacco. "Biophysical groundwork as a hinge to unravel the biology of α-synuclein aggregation and toxicity." Quarterly Reviews of Biophysics 47, no. 1 (January 21, 2014): 1–48. http://dx.doi.org/10.1017/s0033583513000097.

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AbstractAlpha-synuclein (aS) and its aggregation properties are central in the development and spread of Parkinson's disease. Point mutations and multiplications of the SNCA gene encoding aS cause autosomal dominant forms of the disorder. Moreover, protein inclusions found in the surviving neurons of parkinsonian brains consist mainly of a fibrillar form of aS. Aggregates of aS, which form a transient, complex and heterogeneous ensemble, participate in a wide variety of toxic mechanisms that may be amplified by aS spreading among neighbouring neurons. Recently, significant effort has been directed into the study of the aS aggregation process and the impact of aS aggregates on neuron survival. In this review, we present state-of-the-art biophysical studies on the aS aggregation process in vitro and in cellular models. We comprehensively review the new insights generated by the recent biophysical investigations, which could provide a solid basis from which to design future biomedical studies. The diverse cellular models of aS toxicity and their potential use in the biophysical investigation are also discussed.

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10

Fukuoka, Satoshi, Walter Richter, Jörg Howe, Jörg Andrä, Manfred Rössle, Christian Alexander, Thomas Gutsmann, and Klaus Brandenburg. "Biophysical investigations into the interactions of endotoxins with bile acids." Innate Immunity 18, no. 2 (September 27, 2011): 307–17. http://dx.doi.org/10.1177/1753425911404093.

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11

Oberwinkler, J. "TRPM3, a biophysical enigma?" Biochemical Society Transactions 35, no. 1 (January 22, 2007): 89–90. http://dx.doi.org/10.1042/bst0350089.

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TRPM3 [TRP (transient receptor potential) melastatin 3] is one of the least investigated proteins of the TRP family of ion channels. Heterologously expressed TRPM3 channels are constitutively active, have an outwardly rectifying current–voltage relationship and are inhibited by intracellular Mg2+ ions. Besides these rather common features, in which TRPM3 channels resemble the closely related channels TRPM6 and TRPM7, TRPM3 channels have several unique characteristics. The TRPM3 gene encodes a plethora of different proteins owing to alternative splicing and alternative exon usage. One site of alternative splicing affects the ion-conducting pore region and profoundly alters the pore properties of the encoded channels. The channels having the longer pore region efficiently conduct univalent cations, but are only poorly permeated by bivalent cations. Conversely, the channels with the shorter pore region are highly permeable to bivalent cations. Unusually, the short-pore TRPM3 channels are inhibited by extracellular Na+ ions. At physiological sodium concentration, this block is very strong, making it difficult to envision a physiological function for these ion channels. Recently, pharmacological investigations have been initiated in order to identify substances that influence TRPM3 channel activity. With the use of such substances, it might be possible to identify TRPM3 channels in their native environment and to elucidate some of their physiological roles. Hopefully, TRPM3 channels will then no longer appear to be as enigmatic as they do right now.

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12

Hishimoto, Kumio, M. Hisatomi, Y. Miyazaki, E. Yarabu, K. Tsuji, and K. Yamaguchi. "Biophysical Investigations with the Carbon Dioxide Laser -(1) Hepatic Injury Threshold." JOURNAL OF JAPAN SOCIETY FOR LASER SURGERY AND MEDICINE 13, Supplement (1992): 317–20. http://dx.doi.org/10.2530/jslsm1980.13.supplement_317.

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13

Hishimoto, Kumio, M. Hisatomi, Y. Miyazaki, K. Tsuji, and K. Yamaguchi. "Biophysical Investigations with the Carbon Dioxide Laser-(2) Leaf Injury Threshold." JOURNAL OF JAPAN SOCIETY FOR LASER SURGERY AND MEDICINE 15, Supplement (1994): 69–72. http://dx.doi.org/10.2530/jslsm1980.15.supplement_69.

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14

Dario Carugo, Lorenzo Capretto, Eric Nehru, Mohamed Mansour, Neil Smyth, Neil Bressloff, and Xunli Zhang. "A Microfluidic-Based Arteriolar Network Model for Biophysical and Bioanalytical Investigations." Current Analytical Chemistry 9, no. 1 (December 4, 2012): 47–59. http://dx.doi.org/10.2174/1573411011309010047.

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15

Carugo, Dario, Lorenzo Capretto, Eric Nehru, Mohamed Mansour, Neil Smyth, Neil Bressloff, and Xunli Zhang. "A Microfluidic-Based Arteriolar Network Model for Biophysical and Bioanalytical Investigations." Current Analytical Chemistry 9, no. 1 (January 1, 2013): 47–59. http://dx.doi.org/10.2174/157341113804486437.

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16

Choudhary, Sinjan, Shreyada N. Save, Nand Kishore, and Ramakrishna V. Hosur. "Synergistic Inhibition of Protein Fibrillation by Proline and Sorbitol: Biophysical Investigations." PLOS ONE 11, no. 11 (November 21, 2016): e0166487. http://dx.doi.org/10.1371/journal.pone.0166487.

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17

Yadavalli, Vamsi K., and Christopher J. Ehrhardt. "Atomic force microscopy as a biophysical tool for nanoscale forensic investigations." Science & Justice 61, no. 1 (January 2021): 1–12. http://dx.doi.org/10.1016/j.scijus.2020.10.004.

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18

Cannella, S. E., V. Y. Ntsogo Enguene, J. C. Karst, A. Hessel, O. Subrini, A. C. Sotomayor-Perez, B. Raynal, D. Ladant, and A. Chenal. "Biophysical investigations of the adenylate cyclase (CyaA) toxin from Bordetella pertussis." Toxicon 116 (June 2016): 80–81. http://dx.doi.org/10.1016/j.toxicon.2016.01.030.

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19

Homble, F. "A fast and high-current voltage clamp device for biophysical investigations." Journal of Physics E: Scientific Instruments 21, no. 11 (November 1988): 1100–1102. http://dx.doi.org/10.1088/0022-3735/21/11/021.

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20

Scott, William G. "Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme." Quarterly Reviews of Biophysics 32, no. 3 (August 1999): 241–84. http://dx.doi.org/10.1017/s003358350000353x.

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1. How do ribozymes work? 2412. The hammerhead RNA as a prototype ribozyme 2422.1 RNA enzymes 2422.2 Satellite self-cleaving RNAs 2422.3 Hammerhead RNAs and hammerhead ribozymes 2443. The chemical mechanism of hammerhead RNA self-cleavage 2463.1 Phosphodiester isomerization via an SN2(P) reaction 2473.2 The canonical role of divalent metal ions in the hammerhead ribozyme reaction 2513.3 The hammerhead ribozyme does not actually require metal ions for catalysis 2543.4 Hammerhead RNA enzyme kinetics 2574. Sequence requirements for hammerhead RNA self-cleavage 2604.1 The conserved core, mutagenesis and functional group modifications 2604.2 Ground-state vs. transition-state effects 2615. The three-dimensional structure of the hammerhead ribozyme 2625.1 Enzyme–inhibitor complexes 2625.2 Enzyme–substrate complex in the initial state 2645.3 Hammerhead ribozyme self-cleavage in the crystal 2645.4 The requirement for a conformational change 2655.5 Capture of conformational intermediates using crystallographic freeze-trapping 2665.6 The structure of a hammerhead ribozyme ‘early’ conformational intermediate 2675.7 The structure of a hammerhead ribozyme ‘later’ conformational intermediate 2685.8 Is the conformational change pH dependent? 2695.9 Isolating the structure of the cleavage product 2715.10 Evidence for and against additional large-scale conformation changes 2745.11 NMR spectroscopic studies of the hammerhead ribozyme 2786. Concluding remarks 2807. Acknowledgements 2818. References 2811. How do ribozymes work? 241The discovery that RNA can be an enzyme (Guerrier-Takada et al. 1983; Zaug & Cech, 1986) has created the fundamental question of how RNA enzymes work. Before this discovery, it was generally assumed that proteins were the only biopolymers that had sufficient complexity and chemical heterogeneity to catalyze biochemical reactions. Clearly, RNA can adopt sufficiently complex tertiary structures that make catalysis possible. How does the three- dimensional structure of an RNA endow it with catalytic activity? What structural and functional principles are unique to RNA enzymes (or ribozymes), and what principles are so fundamental that they are shared with protein enzymes?

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21

Van Dyke, Chris. "Boxing daze – using state-and-transition models to explore the evolution of socio-biophysical landscapes." Progress in Physical Geography: Earth and Environment 39, no. 5 (May 17, 2015): 594–621. http://dx.doi.org/10.1177/0309133315581700.

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Critical physical geography (CPG) proposes to bridge the lingering gap between human and physical geographers. To rejuvenate conversations among different corners of the discipline about the possibility of trans-disciplinary collaboration, CPG must provide unique epistemological, methodological, and conceptual frameworks that human and physical geographers alike will find appealing, relevant, and timely. These should help them perceptively characterize, narrate, and anticipate changes in socio-biophysical landscapes. This paper outlines a conceptual framework that can be harnessed in future CPG studies and reflects on what it means to be a critical geographer. To solve the epistemological dilemmas confronting CPG, this paper demonstrates that state-and-transition models (STMs) can provide a unifying framework to address questions about socio-biophysical landscape evolution. Originally developed to account for nonlinear dynamics in rangeland ecosystems, STMs have been used to analyze a variety of ecological, geomorphic, and hydrological transitions in complex biophysical landscapes. STMs have epistemological commonalities with explanatory frameworks pioneered by political ecologists, and while thus far they have been used to account for complex biophysical dynamics, they can be expanded to accommodate critical investigations of the social dynamics underpinning landscape change. By foregrounding the transitional dynamics of socio-biophysical landscape – a theme that has interested physical and critical human geographers – STMs establish a conceptual space in which to holistically interpret the interacting drivers that underwrite socio-biophysical landscape change.

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22

Liczner, Christopher, Kieran Duke, Gabrielle Juneau, Martin Egli, and Christopher J. Wilds. "Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications." Beilstein Journal of Organic Chemistry 17 (April 28, 2021): 908–31. http://dx.doi.org/10.3762/bjoc.17.76.

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Over the past 25 years, the acceleration of achievements in the development of oligonucleotide-based therapeutics has resulted in numerous new drugs making it to the market for the treatment of various diseases. Oligonucleotides with alterations to their scaffold, prepared with modified nucleosides and solid-phase synthesis, have yielded molecules with interesting biophysical properties that bind to their targets and are tolerated by the cellular machinery to elicit a therapeutic outcome. Structural techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chemically modified oligonucleotides that have been explored for gene silencing.

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23

Laidler, Gita J., and Paul Treitz. "Biophysical remote sensing of arctic environments." Progress in Physical Geography: Earth and Environment 27, no. 1 (March 2003): 44–68. http://dx.doi.org/10.1191/0309133303pp358ra.

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Various remote sensing studies have been conducted to investigate methods and applications of vegetation mapping and analysis in arctic environments. The general purpose of these studies is to extract information on the spatial and temporal distribution of vegetation as required for tundra ecosystem and climate change studies. Because of the recent emphasis on understanding natural systems at large spatial scales, there has been an increasing interest in deriving biophysical variables from satellite data. Satellite remote sensing offers potential for extrapolating, or ‘scaling up’ biophysical measures derived from local sites, to landscape and even regional scales. The most common investigations include mapping spatial vegetation patterns or assessing biophysical tundra characteristics, using medium resolution satellite data. For instance, Landsat TM data have been shown to be useful for broad vegetation mapping and analysis, but not accurately representative of smaller vegetation communities or local spatial variation. It is anticipated, that high spatial resolution remote sensing data, now available from commercial remote sensing satellites, will provide the necessary sampling scale to link field data to remotely sensed reflectance data. As a result, it is expected that these data will improve the representation of biophysical variables over sparsely vegetated regions of the Arctic.

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24

Loosli, Y., R. Luginbuehl, and J. G. Snedeker. "Cytoskeleton reorganization of spreading cells on micro-patterned islands: a functional model." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 368, no. 1920 (June 13, 2010): 2629–52. http://dx.doi.org/10.1098/rsta.2010.0069.

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Predictive numerical models of cellular response to biophysical cues have emerged as a useful quantitative tool for cell biology research. Cellular experiments in silico can augment in vitro and in vivo investigations by filling gaps in what is possible to achieve through ‘wet work’. Biophysics-based numerical models can be used to verify the plausibility of mechanisms regulating tissue homeostasis derived from experiments. They can also be used to explore potential targets for therapeutic intervention. In this perspective article we introduce a single cell model developed towards the design of novel biomaterials to elicit a regenerative cellular response for the repair of diseased tissues. The model is governed by basic mechanisms of cell spreading (lamellipodial and filopodial extension, formation of cell–matrix adhesions, actin reinforcement) and is developed in the context of cellular interaction with functionalized substrates that present defined points of potential adhesion. To provide adequate context, we first review the biophysical underpinnings of the model as well as reviewing existing cell spreading models. We then present preliminary benchmarking of the model against published experiments of cell spreading on micro-patterned substrates. Initial results indicate that our mechanistic model may represent a potentially useful approach in a better understanding of cell interactions with the extracellular matrix.

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25

Bechinger, Burkhard, and Christopher Aisenbrey. "The Polymorphic Nature of Membrane-Active Peptides from Biophysical and Structural Investigations." Current Protein & Peptide Science 13, no. 7 (November 1, 2012): 602–10. http://dx.doi.org/10.2174/138920312804142093.

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26

Kołodziej, Anna, Aleksandra Wesełucha-Birczyńska, Małgorzata Świętek, Łukasz Skalniak, and Marta Błażewicz. "Raman microspectroscopic investigations of polymer nanocomposites: evaluation of physical and biophysical properties." International Journal of Polymeric Materials and Polymeric Biomaterials 68, no. 1-3 (December 31, 2018): 44–52. http://dx.doi.org/10.1080/00914037.2018.1525722.

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27

Mumper, Mary W., Christophe Aurenge, and Ramachandra S. Hosmane. "“Slim” Nucleosides and Nucleotides. I. Synthetic, Structural and Biophysical Investigations of Showdomycins." Journal of Biomolecular Structure and Dynamics 11, no. 5 (April 1994): 1107–31. http://dx.doi.org/10.1080/07391102.1994.10508055.

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28

Munro, James B., and Kelly K. Lee. "Probing Structural Variation and Dynamics in the HIV-1 Env Fusion Glycoprotein." Current HIV Research 16, no. 1 (April 19, 2018): 5–12. http://dx.doi.org/10.2174/1570162x16666171222110025.

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Background: Recent advances in structural characterization of the HIV envelope glycoprotein (Env) have provided a high-resolution glimpse of the architecture of this target for neutralizing antibodies and the machinery responsible for mediating receptor binding and membrane fusion. These structures primarily capture the detailed organization of the receptor-naive, prefusion conformation of Env, but under native solution conditions Env is highly dynamic, sampling multiple conformational states as well as exhibiting local protein flexibility. Methods: Special emphasis is placed on the use of biophysical methods, including single-molecule fluorescence microscopy and hydrogen/deuterium-exchange mass spectrometry. Results: Using novel biophysical approaches, striking isolate-specific differences in Env’s dynamic profile have been revealed that appear to underlie phenotypic differences of the viral isolates such as neutralization sensitivity and CD4 receptor reactivity. Conclusion: Structural studies are complemented by novel biophysical investigations that enable visualization of the dynamics of HIV-1 Env under native conditions. These approaches will also enable us to gain new insights into the mechanisms of action of antibodies and drugs.

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Bechinger, Burkhard, and Christopher Aisenbrey. "Erratum: The Polymorphic Nature of Membrane-Active Peptides from Biophysical and Structural Investigations." Current Protein & Peptide Science 16, no. 6 (July 2, 2015): 571. http://dx.doi.org/10.2174/138920371606150702133734.

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Marquette, Arnaud, and Burkhard Bechinger. "Biophysical Investigations Elucidating the Mechanisms of Action of Antimicrobial Peptides and Their Synergism." Biomolecules 8, no. 2 (April 18, 2018): 18. http://dx.doi.org/10.3390/biom8020018.

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31

Bechinger, Burkhard. "Biophysical investigations of membrane perturbations by polypeptides using solid-state NMR spectroscopy (Review)." Molecular Membrane Biology 17, no. 3 (January 2000): 135–42. http://dx.doi.org/10.1080/09687680050197365.

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32

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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WYLLER, JOHN, PATRICK BLOMQUIST, and GAUTE T. EINEVOLL. "ON THE ORIGIN AND PROPERTIES OF TWO-POPULATION NEURAL FIELD MODELS - A TUTORIAL INTRODUCTION." Biophysical Reviews and Letters 02, no. 01 (January 2007): 79–98. http://dx.doi.org/10.1142/s1793048007000441.

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Neural field models have a long tradition in mathematical neuroscience, and in the present tutorial paper we outline the neurobiological and biophysical origin of such models, in particular two-population field models describing excitatory and inhibitory neurons interacting via nonlocal spatial connections. Results from investigations of such models on the existence and stability of stationary localized activity pulses ('bumps') and generation of stationary spatial and spatiotemporal oscillations through Turing-type instabilities are described.

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Makris, Nikos, Deepak N. Pandya, Joseph J. Normandin, George M. Papadimitriou, Scott L. Rauch, Verne S. Caviness, and David N. Kennedy. "Quantitative DT-MRI Investigations of the Human Cingulum Bundle." CNS Spectrums 7, no. 7 (July 2002): 522–28. http://dx.doi.org/10.1017/s1092852900018071.

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ABSTRACTWhite matter fiber pathways are key structural components of the brain and its functional organization. The limbic system carries a great deal of its anatomic connectivity via the cingulum bundle. By allowing the in vivo delineation of the stem of the major fiber pathway systems, diffusion tensor magnetic resonance imaging has opened a new window into the detailed structure of the white matter in health and disease. Topographic, biophysical, and volumetric information about fiber tracts will provide a more complete understanding of the brain. By appreciating its interconnections, the precise anatomical knowledge of the cingulum bundle will improve our understanding of the limbic system and may enable improvements in the assessment and treatment of neuropsychiatric disorders. In this study, the stem of the cingulum bundle was investigated and defined in terms of its trajectory, anisotropy, and volume, in four normal human subjects, using diffusion tensor imaging.

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35

Rexford, Alix, Diego A. R. Zorio, and Brian G. Miller. "Biochemical and biophysical investigations of the interaction between human glucokinase and pro-apoptotic BAD." PLOS ONE 12, no. 2 (February 9, 2017): e0171587. http://dx.doi.org/10.1371/journal.pone.0171587.

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36

Morton, Leslie A., Ryo Tamura, Armando J. de Jesus, Arianna Espinoza, and Hang Yin. "Biophysical investigations with MARCKS-ED: dissecting the molecular mechanism of its curvature sensing behaviors." Biochimica et Biophysica Acta (BBA) - Biomembranes 1838, no. 12 (December 2014): 3137–44. http://dx.doi.org/10.1016/j.bbamem.2014.08.027.

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37

Duncan, Anna L., Wanling Song, and Mark S. P. Sansom. "Lipid-Dependent Regulation of Ion Channels and G Protein–Coupled Receptors: Insights from Structures and Simulations." Annual Review of Pharmacology and Toxicology 60, no. 1 (January 6, 2020): 31–50. http://dx.doi.org/10.1146/annurev-pharmtox-010919-023411.

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Ion channels and G protein–coupled receptors (GPCRs) are regulated by lipids in their membrane environment. Structural studies combined with biophysical and molecular simulation investigations reveal interaction sites for specific lipids on membrane protein structures. For K channels, PIP2 plays a key role in regulating Kv and Kir channels. Likewise, several recent cryo-EM structures of TRP channels have revealed bound lipids, including PIP2 and cholesterol. Among the pentameric ligand-gated ion channel family, structural and biophysical studies suggest the M4 TM helix may act as a lipid sensor, e.g., forming part of the binding sites for neurosteroids on the GABAA receptor. Structures of GPCRs have revealed multiple cholesterol sites, which may modulate both receptor dynamics and receptor oligomerization. PIP2 also interacts with GPCRs and may modulate their interactions with G proteins. Overall, it is evident that multiple lipid binding sites exist on channels and receptors that modulate their function allosterically and are potential druggable sites.

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Liang, Zhongjie, Gennady M. Verkhivker, and Guang Hu. "Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications." Briefings in Bioinformatics 21, no. 3 (March 21, 2019): 815–35. http://dx.doi.org/10.1093/bib/bbz029.

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Abstract Proteins are dynamical entities that undergo a plethora of conformational changes, accomplishing their biological functions. Molecular dynamics simulation and normal mode analysis methods have become the gold standard for studying protein dynamics, analyzing molecular mechanism and allosteric regulation of biological systems. The enormous amount of the ensemble-based experimental and computational data on protein structure and dynamics has presented a major challenge for the high-throughput modeling of protein regulation and molecular mechanisms. In parallel, bioinformatics and systems biology approaches including genomic analysis, coevolution and network-based modeling have provided an array of powerful tools that complemented and enriched biophysical insights by enabling high-throughput analysis of biological data and dissection of global molecular signatures underlying mechanisms of protein function and interactions in the cellular environment. These developments have provided a powerful interdisciplinary framework for quantifying the relationships between protein dynamics and allosteric regulation, allowing for high-throughput modeling and engineering of molecular mechanisms. Here, we review fundamental advances in protein dynamics, network theory and coevolutionary analysis that have provided foundation for rapidly growing computational tools for modeling of allosteric regulation. We discuss recent developments in these interdisciplinary areas bridging computational biophysics and network biology, focusing on promising applications in allosteric regulations, including the investigation of allosteric communication pathways, protein–DNA/RNA interactions and disease mutations in genomic medicine. We conclude by formulating and discussing future directions and potential challenges facing quantitative computational investigations of allosteric regulatory mechanisms in protein systems.

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Zaninetti, Carlo, Laura Sachs, and Raghavendra Palankar. "Role of Platelet Cytoskeleton in Platelet Biomechanics: Current and Emerging Methodologies and Their Potential Relevance for the Investigation of Inherited Platelet Disorders." Hämostaseologie 40, no. 03 (July 29, 2020): 337–47. http://dx.doi.org/10.1055/a-1175-6783.

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AbstractCytoskeleton is composed of more than 100 proteins and represents a dynamic network of the cellular cytoplasm. Cytoskeletal functions include spatial organization of cellular components, structural connection of the cell with external environment, and biomechanical force generation. Cytoskeleton takes part, at different levels, in all phases of platelet biogenesis: megakaryocyte (MK) differentiation, MK maturation, and platelet formation. In addition, it also plays a major role in each stage of platelet function. Inherited platelet disorders (IPDs) are a group of rare diseases featured by low platelet count and/or impaired platelet function. Over the past decade, the investigation of platelet biomechanics has become a major and highly relevant theme of research due to its implications at every stage of development of human life. The initial use of diverse biophysical techniques (e.g., micropipette aspiration, atomic force and scanning ion conductance microscopy, real-time deformability cytometry) started unraveling biomechanical features of platelets that are expected to provide new explanations for physiological and pathological mechanisms. Although the impact of cytoskeletal alterations has been largely elucidated in various IPDs' pathogenesis, the understanding of their impact on biomechanical properties of platelets represents an unmet need. Regarding IPDs, improving biomechanical studies seems promising for diagnostic and prognostic implications. Potentially, these characteristics of platelets may also be used for the prediction of bleeding risk. This review addresses the current available methods for biophysical investigations of platelets and the possible implementations in the field of IPDs.

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40

Wilhelmsson, L. Marcus. "Fluorescent nucleic acid base analogues." Quarterly Reviews of Biophysics 43, no. 2 (May 2010): 159–83. http://dx.doi.org/10.1017/s0033583510000090.

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AbstractThe use of fluorescent nucleic acid base analogues is becoming increasingly important in the fields of biology, biochemistry and biophysical chemistry as well as in the field of DNA nanotechnology. The advantage of being able to incorporate a fluorescent probe molecule close to the site of examination in the nucleic acid-containing system of interest with merely a minimal perturbation to the natural structure makes fluorescent base analogues highly attractive. In recent years, there has been a growing interest in developing novel candidates in this group of fluorophores for utilization in various investigations. This review describes the different classes of fluorophores that can be used for studying nucleic acid-containing systems, with an emphasis on choosing the right kind of probe for the system under investigation. It describes the characteristics of the large group of base analogues that has an emission that is sensitive to the surrounding microenvironment and gives examples of investigations in which this group of molecules has been used so far. Furthermore, the characterization and use of fluorescent base analogues that are virtually insensitive to changes in their microenvironment are described in detail. This group of base analogues can be used in several fluorescence investigations of nucleic acids, especially in fluorescence anisotropy and fluorescence resonance energy transfer (FRET) measurements. Finally, the development and characterization of the first nucleic base analogue FRET pair, tCO–tCnitro, and its possible future uses are discussed.

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Scifoni, Emanuele. "Radiation biophysical aspects of charged particles: From the nanoscale to therapy." Modern Physics Letters A 30, no. 17 (May 22, 2015): 1540019. http://dx.doi.org/10.1142/s0217732315400192.

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Charged particle applications for radiotherapy are motivated by their specific advantages in terms of dose delivery and biological effect. These advantages have to a large extent originated from the peculiarities of ion beam energy deposition patterns in the medium on a microscopic, down to a nanoscopic scale. A large amount of research was conducted in this direction, especially in the last two decades, profiting also from the parallel investigations going on in radiation protection for space exploration. The main biophysical aspects of charged particles, which are relevant to hadrontherapy are shortly reviewed in the present contribution, namely focusing on relative biological effectiveness (RBE), oxygen enhancement ratio (OER) and combination with radiosensitizers. A summary of present major research direction on both microscopic and macroscopic assessment of the specific mechanism of radiation damage will be given, as well as several open challenges for a better understanding of the whole process, which still limit the full exploitation of ion beams for radiotherapy.

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Bechinger, Burkhard. "Insights into the mechanisms of action of host defence peptides from biophysical and structural investigations." Journal of Peptide Science 17, no. 5 (February 28, 2011): 306–14. http://dx.doi.org/10.1002/psc.1343.

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Bechinger, Burkhard. "Insights into the mechanisms of action of host defence peptides from biophysical and structural investigations." Journal of Peptide Science 21, no. 8 (July 22, 2015): 689. http://dx.doi.org/10.1002/psc.2799.

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Correa, Wilmar, Lena Heinbockel, Kerstin Stephan, and Thomas Gutsmann. "Biophysical Investigations on the Interaction between Antimicrobial Peptides and Bacteria Killed by Cs-137 Irradiation." Biophysical Journal 110, no. 3 (February 2016): 79a. http://dx.doi.org/10.1016/j.bpj.2015.11.490.

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Sánchez-Martín, Maria Jesús, Patricia Urbán, Montserrat Pujol, Isabel Haro, M. Asunción Alsina, and M. Antònia Busquets. "Biophysical Investigations of GBV-C E1 Peptides as Potential Inhibitors of HIV-1 Fusion Peptide." ChemPhysChem 12, no. 15 (September 8, 2011): 2816–22. http://dx.doi.org/10.1002/cphc.201100407.

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Koch, Marion, Katherine E. Wright, Oliver Otto, Maik Herbig, Nichole D. Salinas, Niraj H. Tolia, Timothy J. Satchwell, Jochen Guck, Nicholas J. Brooks, and Jake Baum. "Plasmodium falciparum erythrocyte-binding antigen 175 triggers a biophysical change in the red blood cell that facilitates invasion." Proceedings of the National Academy of Sciences 114, no. 16 (April 3, 2017): 4225–30. http://dx.doi.org/10.1073/pnas.1620843114.

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Invasion of the red blood cell (RBC) by the Plasmodium parasite defines the start of malaria disease pathogenesis. To date, experimental investigations into invasion have focused predominantly on the role of parasite adhesins or signaling pathways and the identity of binding receptors on the red cell surface. A potential role for signaling pathways within the erythrocyte, which might alter red cell biophysical properties to facilitate invasion, has largely been ignored. The parasite erythrocyte-binding antigen 175 (EBA175), a protein required for entry in most parasite strains, plays a key role by binding to glycophorin A (GPA) on the red cell surface, although the function of this binding interaction is unknown. Here, using real-time deformability cytometry and flicker spectroscopy to define biophysical properties of the erythrocyte, we show that EBA175 binding to GPA leads to an increase in the cytoskeletal tension of the red cell and a reduction in the bending modulus of the cell’s membrane. We isolate the changes in the cytoskeleton and membrane and show that reduction in the bending modulus is directly correlated with parasite invasion efficiency. These data strongly imply that the malaria parasite primes the erythrocyte surface through its binding antigens, altering the biophysical nature of the target cell and thus reducing a critical energy barrier to invasion. This finding would constitute a major change in our concept of malaria parasite invasion, suggesting it is, in fact, a balance between parasite and host cell physical forces working together to facilitate entry.

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Navaee, Fatemeh, Philippe Renaud, Alexander Kleger, and Thomas Braschler. "Highly Efficient Cardiac Differentiation and Maintenance by Thrombin-Coagulated Fibrin Hydrogels Enriched with Decellularized Porcine Heart Extracellular Matrix." International Journal of Molecular Sciences 24, no. 3 (February 2, 2023): 2842. http://dx.doi.org/10.3390/ijms24032842.

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Biochemical and biophysical properties instruct cardiac tissue morphogenesis. Here, we are reporting on a blend of cardiac decellularized extracellular matrix (dECM) from porcine ventricular tissue and fibrinogen that is suitable for investigations employing an in vitro 3D cardiac cell culture model. Rapid and specific coagulation with thrombin facilitates the gentle inclusion of cells while avoiding sedimentation during formation of the dECM-fibrin composite. Our investigations revealed enhanced cardiogenic differentiation in the H9c2 myoblast cells when using the system in a co-culture with Nor-10 fibroblasts. Further enhancement of differentiation efficiency was achieved by 3D embedding of rat neonatal cardiomyocytes in the 3D system. Calcium imaging and analysis of beating motion both indicate that the dECM-fibrin composite significantly enhances recovery, frequency, synchrony, and the maintenance of spontaneous beating, as compared to various controls including Matrigel, pure fibrin and collagen I as well as a fibrin-collagen I blend.

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Ami, Diletta, Barbara Sciandrone, Paolo Mereghetti, Jacopo Falvo, Tiziano Catelani, Cristina Visentin, Paolo Tortora, Salvador Ventura, Antonino Natalello, and Maria Elena Regonesi. "Pathological ATX3 Expression Induces Cell Perturbations in E. coli as Revealed by Biochemical and Biophysical Investigations." International Journal of Molecular Sciences 22, no. 2 (January 19, 2021): 943. http://dx.doi.org/10.3390/ijms22020943.

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Amyloid aggregation of human ataxin-3 (ATX3) is responsible for spinocerebellar ataxia type 3, which belongs to the class of polyglutamine neurodegenerative disorders. It is widely accepted that the formation of toxic oligomeric species is primarily involved in the onset of the disease. For this reason, to understand the mechanisms underlying toxicity, we expressed both a physiological (ATX3-Q24) and a pathological ATX3 variant (ATX3-Q55) in a simplified cellular model, Escherichia coli. It has been observed that ATX3-Q55 expression induces a higher reduction of the cell growth compared to ATX3-Q24, due to the bacteriostatic effect of the toxic oligomeric species. Furthermore, the Fourier transform infrared microspectroscopy investigation, supported by multivariate analysis, made it possible to monitor protein aggregation and the induced cell perturbations in intact cells. In particular, it has been found that the toxic oligomeric species associated with the expression of ATX3-Q55 are responsible for the main spectral changes, ascribable mainly to the cell envelope modifications. A structural alteration of the membrane detected through electron microscopy analysis in the strain expressing the pathological form supports the spectroscopic results.

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WARD, Roberta J., Anne L. FLORENCE, Dianne BALDWIN, Clifford ABIAKA, Francine ROLAND, Michael H. RAMSEY, Dominic P. E. DICKSON, Timothy J. PETERS, and Robert R. CRICHTON. "Biochemical and biophysical investigations of the ferrocene-iron-loaded rat. An animal model of primary haemochromatosis." European Journal of Biochemistry 202, no. 2 (December 1991): 405–10. http://dx.doi.org/10.1111/j.1432-1033.1991.tb16389.x.

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Ries, Annika, Rajesh Kumar, Chenguang Lou, Tamer Kosbar, Empar Vengut-Climent, Per T. Jørgensen, Juan C. Morales, and Jesper Wengel. "Synthesis and Biophysical Investigations of Oligonucleotides Containing Galactose-Modified DNA, LNA, and 2′-Amino-LNA Monomers." Journal of Organic Chemistry 81, no. 22 (October 25, 2016): 10845–56. http://dx.doi.org/10.1021/acs.joc.6b01917.

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