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Evidence of zoonotic pathogens through biophysically induced genomic variance Q. Rev. Biophys. (IF 6.1) Pub Date : 2024-03-13 Daniah Alsufyani
Zoonoses are infectious agents that are transmissible between animals and humans. Up to 60% of known infectious diseases and 75% of emergent diseases are zoonotic. Genomic variation between homeostatic populations provides a novel window into the effect of environmental pathogens on allelic distributions within the populations. Genodynamics is a biophysical approach utilizing developed metrics on biallelic
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Optogenetic control of neural activity: The biophysics of microbial rhodopsins in neuroscience Q. Rev. Biophys. (IF 6.1) Pub Date : 2023-10-13 Kiryl D. Piatkevich, Edward S. Boyden
Optogenetics, the use of microbial rhodopsins to make the electrical activity of targeted neurons controllable by light, has swept through neuroscience, enabling thousands of scientists to study how specific neuron types contribute to behaviors and pathologies, and how they might serve as novel therapeutic targets. By activating a set of neurons, one can probe what functions they can initiate or sustain
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Single-molecule FRET for virology: 20 years of insight into protein structure and dynamics Q. Rev. Biophys. (IF 6.1) Pub Date : 2023-05-18 Danielle Groves, Christof Hepp, Achillefs N. Kapanidis, Nicole C. Robb
Although viral protein structure and replication mechanisms have been explored extensively with X-ray crystallography, cryo-electron microscopy, and population imaging studies, these methods are often not able to distinguish dynamic conformational changes in real time. Single-molecule fluorescence resonance energy transfer (smFRET) offers unique insights into interactions and states that may be missed
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Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling Q. Rev. Biophys. (IF 6.1) Pub Date : 2023-01-11 Bin Sun, Peter M. Kekenes-Huskey
The cardiac sarcomere is a cellular structure in the heart that enables muscle cells to contract. Dozens of proteins belong to the cardiac sarcomere, which work in tandem to generate force and adapt to demands on cardiac output. Intriguingly, the majority of these proteins have significant intrinsic disorder that contributes to their functions, yet the biophysics of these intrinsically disordered regions
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Ferric heme b in aqueous micellar and vesicular systems: state-of-the-art and challenges Q. Rev. Biophys. (IF 6.1) Pub Date : 2023-01-11 Nemanja Cvjetan, Peter Walde
Ferric heme b (= ferric protoporphyrin IX = hemin) is an important prosthetic group of different types of enzymes, including the intensively investigated and widely applied horseradish peroxidase (HRP). In HRP, hemin is present in monomeric form in a hydrophobic pocket containing among other amino acid side chains the two imidazoyl groups of His170 and His42. Both amino acids are important for the
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Nobel Prize 2022 to Sharpless, Meldal, Bertozzi Click Chemistry - molecular lego. Q. Rev. Biophys. (IF 6.1) Pub Date : 2022-11-07 Tom Brown,Bengt Nordén
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DNA in nanochannels: theory and applications Q. Rev. Biophys. (IF 6.1) Pub Date : 2022-10-07 Karolin Frykholm, Vilhelm Müller, Sriram KK, Kevin D. Dorfman, Fredrik Westerlund
Nanofluidic structures have over the last two decades emerged as a powerful platform for detailed analysis of DNA on the kilobase pair length scale. When DNA is confined to a nanochannel, the combination of excluded volume and DNA stiffness leads to the DNA being stretched to near its full contour length. Importantly, this stretching takes place at equilibrium, without any chemical modifications to
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Tryptophan, more than just an interfacial amino acid in the membrane activity of cationic cell-penetrating and antimicrobial peptides Q. Rev. Biophys. (IF 6.1) Pub Date : 2022-08-18 Sonia Khemaissa, Astrid Walrant, Sandrine Sagan
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Determination of protein–protein interactions at the single-molecule level using optical tweezers Q. Rev. Biophys. (IF 6.1) Pub Date : 2022-08-10 Wendy N. Sánchez, Luka Robeson, Valentina Carrasco, Nataniel L. Figueroa, Francesca Burgos-Bravo, Christian A. M. Wilson, Nathalie Casanova-Morales
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The development of single molecule force spectroscopy: from polymer biophysics to molecular machines Q. Rev. Biophys. (IF 6.1) Pub Date : 2022-08-02 Carlos Bustamante, Shannon Yan
The advent of single-molecule force spectroscopy represents the introduction of forces, torques, and displacements as controlled variables in biochemistry. These methods afford the direct manipulation of individual molecules to interrogate the forces that hold together their structure, the forces and torques that these molecules generate in the course of their biochemical reactions, and the use of
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Hiding in plain sight: three chemically distinct α-helix types Q. Rev. Biophys. (IF 6.1) Pub Date : 2022-06-20 Shuguang Zhang, Martin Egli
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When Alphafold2 predictions go wrong for protein–protein complexes, is there something to be learnt? Q. Rev. Biophys. (IF 6.1) Pub Date : 2022-06-15 Juliette Martin
In this short communication, I analyze cases of failed predictions for protein–protein complexes with Alphafold2, and show that they either point to erroneous annotation in the PDB or correct binding site regions.
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Digging into the biophysical features of cell membranes with lipid-DNA conjugates Q. Rev. Biophys. (IF 6.1) Pub Date : 2022-05-16 Ahsan Ausaf Ali, Yousef Bagheri, Mingxu You
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Use of vector formalism in the analysis of hydrophobic and electric driving forces in biological assemblies Q. Rev. Biophys. (IF 6.1) Pub Date : 2022-04-11 Angel Mozo-Villarías, Juan A. Cedano, Enrique Querol
Hydrophobic forces are known to have a crucial part not only in the conformation of the three-dimensional structure of proteins, but also in the build-up of DNA–protein complexes. Electric forces also play an important role both in the tertiary as well in the quaternary structure of macromolecular associations. Sometimes both hydrophobic and electric interactions add up their strengths to accomplish
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Studies of cell-penetrating peptides by biophysical methods Q. Rev. Biophys. (IF 6.1) Pub Date : 2022-04-11 Matjaž Zorko, Ülo Langel
Biophysical studies have a very high impact on the understanding of internalization, molecular mechanisms, interactions, and localization of CPPs and CPP/cargo conjugates in live cells or in vivo. Biophysical studies are often first carried out in test-tube set-ups or in vitro, leading to the complicated in vivo systems. This review describes recent studies of CPP internalization, mechanisms, and localization
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Structures of synthetic helical filaments and tubes based on peptide and peptido-mimetic polymers Q. Rev. Biophys. (IF 6.1) Pub Date : 2022-03-21 Jessalyn G. Miller, Spencer A. Hughes, Charles Modlin, Vincent P. Conticello
Synthetic peptide and peptido-mimetic filaments and tubes represent a diverse class of nanomaterials with a broad range of potential applications, such as drug delivery, vaccine development, synthetic catalyst design, encapsulation, and energy transduction. The structures of these filaments comprise supramolecular polymers based on helical arrangements of subunits that can be derived from self-assembly
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Differential repair enzyme-substrate selection within dynamic DNA energy landscapes Q. Rev. Biophys. (IF 6.1) Pub Date : 2021-12-06 J. Völker, K. J. Breslauer
We demonstrate that reshaping of the dynamic, bulged-loop energy landscape of DNA triplet repeat ensembles by the presence of an abasic site alters repair outcomes by the APE1 enzyme. This phenomenon depends on the structural context of the lesion, despite the abasic site always having the same neighbors in sequence space. We employ this lesion-induced redistribution of DNA states and a kinetic trap
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The mechanics of mitotic chromosomes Q. Rev. Biophys. (IF 6.1) Pub Date : 2021-09-17 T. Man, H. Witt, E. J. G. Peterman, G. J. L. Wuite
Condensation and faithful separation of the genome are crucial for the cellular life cycle. During chromosome segregation, mechanical forces generated by the mitotic spindle pull apart the sister chromatids. The mechanical nature of this process has motivated a lot of research interest into the mechanical properties of mitotic chromosomes. Although their fundamental mechanical characteristics are known
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A molecular view of DNA flexibility Q. Rev. Biophys. (IF 6.1) Pub Date : 2021-07-06 Alberto Marin-Gonzalez, J. G. Vilhena, Ruben Perez, Fernando Moreno-Herrero
DNA dynamics can only be understood by taking into account its complex mechanical behavior at different length scales. At the micrometer level, the mechanical properties of single DNA molecules have been well-characterized by polymer models and are commonly quantified by a persistence length of 50 nm (~150 bp). However, at the base pair level (~3.4 Å), the dynamics of DNA involves complex molecular
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Where in the cell is my protein? Q. Rev. Biophys. (IF 6.1) Pub Date : 2021-06-21 David J. DeRosier
The application of cryo-correlative light and cryo-electron microscopy (cryo-CLEM) gives us a way to locate structures of interest in the electron microscope. In brief, the structures of interest are fluorescently tagged, and images from the cryo-fluorescent microscope (cryo-FM) maps are superimposed on those from the cryo-electron microscope (cryo-EM). By enhancing cryo-FM to include single-molecule
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Amphipathic environments for determining the structure of membrane proteins by single-particle electron cryo-microscopy Q. Rev. Biophys. (IF 6.1) Pub Date : 2021-03-31 Christel Le Bon, Baptiste Michon, Jean-Luc Popot, Manuela Zoonens
Over the past decade, the structural biology of membrane proteins (MPs) has taken a new turn thanks to epoch-making technical progress in single-particle electron cryo-microscopy (cryo-EM) as well as to improvements in sample preparation. The present analysis provides an overview of the extent and modes of usage of the various types of surfactants for cryo-EM studies. Digitonin, dodecylmaltoside, protein-based
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A quantitative model of a cooperative two-state equilibrium in DNA: experimental tests, insights, and predictions Q. Rev. Biophys. (IF 6.1) Pub Date : 2021-03-16 J. Michael Schurr
Quantitative parameters for a two-state cooperative transition in duplex DNAs were finally obtained during the last 5 years. After a brief discussion of observations pertaining to the existence of the two-state equilibrium per se, the lengths, torsion, and bending elastic constants of the two states involved and the cooperativity parameter of the model are simply stated. Experimental tests of model
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Current limitations to high-resolution structure determination by single-particle cryoEM Q. Rev. Biophys. (IF 6.1) Pub Date : 2021-03-11 Edoardo D'Imprima, Werner Kühlbrandt
CryoEM has become the method of choice for determining the structure of large macromolecular complexes in multiple conformations, at resolutions where unambiguous atomic models can be built. Two effects that have limited progress in single-particle cryoEM are (i) beam-induced movement during image acquisition and (ii) protein adsorption and denaturation at the air-water interface during specimen preparation
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Hydrophobic interactions control the self-assembly of DNA and cellulose Q. Rev. Biophys. (IF 6.1) Pub Date : 2021-02-05 Björn Lindman, Bruno Medronho, Luís Alves, Magnus Norgren, Lars Nordenskiöld
Desoxyribosenucleic acid, DNA, and cellulose molecules self-assemble in aqueous systems. This aggregation is the basis of the important functions of these biological macromolecules. Both DNA and cellulose have significant polar and nonpolar parts and there is a delicate balance between hydrophilic and hydrophobic interactions. The hydrophilic interactions related to net charges have been thoroughly
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Macromolecular room temperature crystallography Q. Rev. Biophys. (IF 6.1) Pub Date : 2021-01-08 Marcus Fischer
X-ray crystallography enables detailed structural studies of proteins to understand and modulate their function. Conducting crystallographic experiments at cryogenic temperatures has practical benefits but potentially limits the identification of functionally important alternative protein conformations that can be revealed only at room temperature (RT). This review discusses practical aspects of preparing
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Setting up and operating a cryo-EM laboratory Q. Rev. Biophys. (IF 6.1) Pub Date : 2021-01-08 Deryck J. Mills
Cryo-electron microscopy (cryo-EM) has become the technique of choice for structural biology of macromolecular assemblies, after the ‘resolution revolution’ that has occurred in this field since 2012. With a suitable instrument, an appropriate electron detector and, last but not least, a cooperative sample it is now possible to collect images from which macromolecular structures can be determined to
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Energy mapping of the genetic code and genomic domains: implications for code evolution and molecular Darwinism - CORRIGENDUM. Q. Rev. Biophys. (IF 6.1) Pub Date : 2020-12-10 Horst H Klump,Jens Völker,Kenneth J Breslauer
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Biophysical studies of protein misfolding and aggregation in in vivo models of Alzheimer's and Parkinson's diseases - ERRATUM. Q. Rev. Biophys. (IF 6.1) Pub Date : 2020-11-18 Tessa Sinnige,Karen Stroobants,Christopher M Dobson,Michele Vendruscolo
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Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives Q. Rev. Biophys. (IF 6.1) Pub Date : 2020-11-05 Jinming Wu, Chan Cao, Rolf Antonie Loch, Ann Tiiman, Jinghui Luo
In neurodegenerative diseases, a wide range of amyloid proteins or peptides such as amyloid-beta and α-synuclein fail to keep native functional conformations, followed by misfolding and self-assembling into a diverse array of aggregates. The aggregates further exert toxicity leading to the dysfunction, degeneration and loss of cells in the affected organs. Due to the disordered structure of the amyloid
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Energy mapping of the genetic code and genomic domains: implications for code evolution and molecular Darwinism Q. Rev. Biophys. (IF 6.1) Pub Date : 2020-11-04 Horst H. Klump, Jens Völker, Kenneth J. Breslauer
When the iconic DNA genetic code is expressed in terms of energy differentials, one observes that information embedded in chemical sequences, including some biological outcomes, correlate with distinctive free energy profiles. Specifically, we find correlations between codon usage and codon free energy, suggestive of a thermodynamic selection for codon usage. We also find correlations between what
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Exploring the dynamics of flagellar dynein within the axoneme with Fluctuating Finite Element Analysis Q. Rev. Biophys. (IF 6.1) Pub Date : 2020-08-10 Robin A. Richardson, Benjamin S. Hanson, Daniel J. Read, Oliver G. Harlen, Sarah A. Harris
Flagellar dyneins are the molecular motors responsible for producing the propagating bending motions of cilia and flagella. They are located within a densely packed and highly organised super-macromolecular cytoskeletal structure known as the axoneme. Using the mesoscale simulation technique Fluctuating Finite Element Analysis (FFEA), which represents proteins as viscoelastic continuum objects subject
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Engineering polymerases for applications in synthetic biology Q. Rev. Biophys. (IF 6.1) Pub Date : 2020-07-27 Ali Nikoomanzar, Nicholas Chim, Eric J. Yik, John C. Chaput
DNA polymerases play a central role in biology by transferring genetic information from one generation to the next during cell division. Harnessing the power of these enzymes in the laboratory has fueled an increase in biomedical applications that involve the synthesis, amplification, and sequencing of DNA. However, the high substrate specificity exhibited by most naturally occurring DNA polymerases
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Survival of the cheapest: how proteome cost minimization drives evolution Q. Rev. Biophys. (IF 6.1) Pub Date : 2020-06-23 Kasper P. Kepp
Darwin's theory of evolution emphasized that positive selection of functional proficiency provides the fitness that ultimately determines the structure of life, a view that has dominated biochemical thinking of enzymes as perfectly optimized for their specific functions. The 20th-century modern synthesis, structural biology, and the central dogma explained the machinery of evolution, and nearly neutral
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Confined molecules: experiment meets theory in small spaces Q. Rev. Biophys. (IF 6.1) Pub Date : 2020-06-22 Yang Yu, Julius Rebek
The behavior of molecules confined to small spaces is fascinating chemistry and lies at the heart of signaling processes in biology. Our approach to confinement is through reversible encapsulation of small molecules in synthetic containers. We show that confinement leads to amplified reactivities in bimolecular reactions, stabilization of otherwise reactive species, and limitation in motions that create
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Biophysical studies of protein misfolding and aggregation inin vivomodels of Alzheimer's and Parkinson's diseases Q. Rev. Biophys. (IF 6.1) Pub Date : 2020-06-04 Tessa Sinnige, Karen Stroobants, Christopher M. Dobson, Michele Vendruscolo
Neurodegenerative disorders, including Alzheimer's (AD) and Parkinson's diseases (PD), are characterised by the formation of aberrant assemblies of misfolded proteins. The discovery of disease-modifying drugs for these disorders is challenging, in part because we still have a limited understanding of their molecular origins. In this review, we discuss how biophysical approaches can help explain the
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Anionic food color tartrazine enhances antibacterial efficacy of histatin-derived peptide DHVAR4 by fine-tuning its membrane activity Q. Rev. Biophys. (IF 6.1) Pub Date : 2020-03-02 Maria Ricci, Kata Horváti, Tünde Juhász, Imola Szigyártó, György Török, Fanni Sebák, Andrea Bodor, László Homolya, Judit Henczkó, Bernadett Pályi, Tamás Mlinkó, Judith Mihály, Bilal Nizami, Zihuayuan Yang, Fengming Lin, Xiaolin Lu, Loránd Románszki, Attila Bóta, Zoltán Varga, Szilvia Bősze, Ferenc Zsila, Tamás Beke-Somfai
Here it is demonstrated how some anionic food additives commonly used in our diet, such as tartrazine (TZ), bind to DHVAR4, an antimicrobial peptide (AMP) derived from oral host defense peptides, resulting in significantly fostered toxic activity against both Gram-positive and Gram-negative bacteria, but not against mammalian cells. Biophysical studies on the DHVAR4–TZ interaction indicate that initially
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Chaperonin-assisted protein folding: a chronologue Q. Rev. Biophys. (IF 6.1) Pub Date : 2020-02-19 Arthur L. Horwich, Wayne A. Fenton
This chronologue seeks to document the discovery and development of an understanding of oligomeric ring protein assemblies known as chaperonins that assist protein folding in the cell. It provides detail regarding genetic, physiologic, biochemical, and biophysical studies of these ATP-utilizing machines from bothin vivoandin vitroobservations. The chronologue is organized into various topics of physiology
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De novoprotein design, a retrospective Q. Rev. Biophys. (IF 6.1) Pub Date : 2020-02-11 Ivan V. Korendovych, William F. DeGrado
Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, orde novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing
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Off-pathway 3D-structure provides protection against spontaneous Asn/Asp isomerization: shielding proteins Achilles heel Q. Rev. Biophys. (IF 6.1) Pub Date : 2020-01-31 András Láng, Imre Jákli, Kata Nóra Enyedi, Gábor Mező, Dóra K. Menyhárd, András Perczel
Spontaneous deamidation prompted backbone isomerization of Asn/Asp residues resulting in – most cases – the insertion of an extra methylene group into the backbone poses a threat to the structural integrity of proteins. Here we present a systematical analysis of how temperature, pH, presence of charged residues, but most importantly backbone conformation and dynamics affect isomerization rates as determined
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In cellulo FRET-FLIM and single molecule tracking reveal the supra-molecular organization of the pyoverdine bio-synthetic enzymes in Pseudomonas aeruginosa Q. Rev. Biophys. (IF 6.1) Pub Date : 2020-01-09 Véronique Gasser, Morgane Malrieu, Anne Forster, Yves Mély, Isabelle J. Schalk, Julien Godet
The bio-synthesis of pyoverdine (PVD) in Pseudomonas aeruginosa involves multiple enzymatic steps including the action of non-ribosomal peptide synthetases (NRPSs). One hallmark of NRPS is their ability to make usage of non-proteinogenic amino-acids synthesized by co-expressed accessory enzymes. It is generally proposed that different enzymes of a secondary metabolic pathway assemble into large supra-molecular
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Structure and function of the endothelial surface layer: unraveling the nanoarchitecture of biological surfaces Q. Rev. Biophys. (IF 6.1) Pub Date : 2019-11-27 Brandon P. Reines, Barry W. Ninham
Among the unsolved mysteries of modern biology is the nature of a lining of blood vessels called the ‘endothelial surface layer’ or ESL. In venous micro-vessels, it is half a micron in thickness. The ESL is 10 times thicker than the endothelial glycocalyx (eGC) at its base, has been presumed to be comprised mainly of water, yet is rigid enough to exclude red blood cells. How is this possible? Developments
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The biophysics of superoxide dismutase-1 and amyotrophic lateral sclerosis Q. Rev. Biophys. (IF 6.1) Pub Date : 2019-11-25 Gareth S. A. Wright, Svetlana V. Antonyuk, S. Samar Hasnain
Few proteins have come under such intense scrutiny as superoxide dismutase-1 (SOD1). For almost a century, scientists have dissected its form, function and then later its malfunction in the neurodegenerative disease amyotrophic lateral sclerosis (ALS). We now know SOD1 is a zinc and copper metalloenzyme that clears superoxide as part of our antioxidant defence and respiratory regulation systems. The
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The behavior of ions in water is controlled by their water affinity Q. Rev. Biophys. (IF 6.1) Pub Date : 2019-11-18 Kim D. Collins
The strong, long-range electrostatic forces described by Coulomb's law disappear for ions in water, and the behavior of these ions is instead controlled by their water affinity – a weak, short-range force which arises from their charge density. This was established experimentally in the mid-1980s by size-exclusion chromatography on carefully calibrated Sephadex®G-10 (which measures the effective volume
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Regulation of cell adhesion: a collaborative effort of integrins, their ligands, cytoplasmic actors, and phosphorylation Q. Rev. Biophys. (IF 6.1) Pub Date : 2019-11-11 Carl G. Gahmberg, Mikaela Grönholm, Sudarrshan Madhavan, Farhana Jahan, Esa Mikkola, Larisa Viazmina, Erkki Koivunen
Integrins are large heterodimeric type 1 membrane proteins expressed in all nucleated mammalian cells. Eighteenα-chains and eightβ-chains can combine to form 24 different integrins. They are cell adhesion proteins, which bind to a large variety of cellular and extracellular ligands. Integrins are required for cell migration, hemostasis, translocation of cells out from the blood stream and further movement
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DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase - CORRIGENDUM. Q. Rev. Biophys. (IF 6.1) Pub Date : 2018-01-10 Amirhossein Taghavi,Paul van der Schoot,Joshua T Berryman
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Former QRB Editor Richard Henderson awarded the Nobel Prize. Q. Rev. Biophys. (IF 6.1) Pub Date : 2018-01-01 Bengt Nordén,David Lilley
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QRB Discovery: introducing original research to QRB. Q. Rev. Biophys. (IF 6.1) Pub Date : 2016-09-24 Bengt Nordén
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Navigating at night: fundamental limits on the sensitivity of radical pair magnetoreception under dim light Q. Rev. Biophys. (IF 6.1) Pub Date : 2019-10-22 H. G. Hiscock, T. W. Hiscock, D. R. Kattnig, T. Scrivener, A. M. Lewis, D. E. Manolopoulos, P. J. Hore
Night-migratory songbirds appear to sense the direction of the Earth's magnetic field via radical pair intermediates formed photochemically in cryptochrome flavoproteins contained in photoreceptor cells in their retinas. It is an open question whether this light-dependent mechanism could be sufficiently sensitive given the low-light levels experienced by nocturnal migrants. The scarcity of available
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Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers Q. Rev. Biophys. (IF 6.1) Pub Date : 2019-08-19 Robert J. Trachman, Adrian R. Ferré-D'Amaré
Fluorescence turn-on aptamers,in vitroevolved RNA molecules that bind conditional fluorophores and activate their fluorescence, have emerged as RNA counterparts of the fluorescent proteins. Turn-on aptamers have been selected to bind diverse fluorophores, and they achieve varying degrees of specificity and affinity. These RNA–fluorophore complexes, many of which exceed the brightness of green fluorescent
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Development of CRISPR-Cas systems for genome editing and beyond Q. Rev. Biophys. (IF 6.1) Pub Date : 2019-06-13 F. Zhang
The development of clustered regularly interspaced short-palindromic repeat (CRISPR)-Cas systems for genome editing has transformed the way life science research is conducted and holds enormous potential for the treatment of disease as well as for many aspects of biotechnology. Here, I provide a personal perspective on the development of CRISPR-Cas9 for genome editing within the broader context of
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Dynamics of proteins in solution Q. Rev. Biophys. (IF 6.1) Pub Date : 2019-06-13 Marco Grimaldo, Felix Roosen-Runge, Fajun Zhang, Frank Schreiber, Tilo Seydel
The dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable
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Controlling the movement of molecules Q. Rev. Biophys. (IF 6.1) Pub Date : 2019-05-14 Robert Langer
The ability to control the movement of molecules is both fascinating scientifically as well as being critically important to the well-being of our planet and its people. In particular, the sustained release of molecules over prolonged periods at controlled rates has had and will continue to have enormous implications for the delivery of substances in medicine, agriculture, the environment, nutrition
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Aggregation behavior of the amyloid model peptide NACore Q. Rev. Biophys. (IF 6.1) Pub Date : 2019-04-23 Jon Pallbo, Emma Sparr, Ulf Olsson
The aggregation of the 11 residue long NACore peptide segment of α-synuclein (68-GAVVTGVTAVA-78) has been investigated using a combination of cryogenic transmission electron microscopy (cryo-TEM), small- and wide-angle X-ray scattering, and spectroscopy techniques. The aqueous peptide solubility is pH dependent, and aggregation was triggered by a pH quench from pH 11.3 to approximately pH 8 or 6, where
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The theory of frame ordering: observing motions in calmodulin complexes Q. Rev. Biophys. (IF 6.1) Pub Date : 2019-04-03 Edward James d'Auvergne, Christian Griesinger
Large scale functional motions of molecules are studied experimentally using numerous molecular and biophysics techniques, the data from which are subsequently interpreted using diverse models of Brownian molecular dynamics. To unify all rotational physics techniques and motional models, the frame order tensor – a universal statistical mechanics theory based on the rotational ordering of rigid body
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Annealing of ssDNA and compaction of dsDNA by the HIV-1 nucleocapsid and Gag proteins visualized using nanofluidic channels Q. Rev. Biophys. (IF 6.1) Pub Date : 2019-02-08 Kai Jiang, Nicolas Humbert, Sriram KK, Thiebault Lequeu, Yii-Lih Lin, Yves Mely, Fredrik Westerlund
The nucleocapsid protein NC is a crucial component in the human immunodeficiency virus type 1 life cycle. It functions both in its processed mature form and as part of the polyprotein Gag that plays a key role in the formation of new viruses. NC can protect nucleic acids (NAs) from degradation by compacting them to a dense coil. Moreover, through its NA chaperone activity, NC can also promote the most
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Oxygenic photosynthesis: history, status and perspective Q. Rev. Biophys. (IF 6.1) Pub Date : 2019-01-23 Wolfgang Junge
Cyanobacteria and plants carry out oxygenic photosynthesis. They use water to generate the atmospheric oxygen we breathe and carbon dioxide to produce the biomass serving as food, feed, fibre and fuel. This paper scans the emergence of structural and mechanistic understanding of oxygen evolution over the past 50 years. It reviews speculative concepts and the stepped insight provided by novel experimental
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The enigmatic ribosomal stalk Q. Rev. Biophys. (IF 6.1) Pub Date : 2018-12-21 Anders Liljas, Suparna Sanyal
The large ribosomal subunit has a distinct feature, the stalk, extending outside the ribosome. In bacteria it is called the L12 stalk. The base of the stalk is protein uL10 to which two or three dimers of proteins bL12 bind. In archea and eukarya P1 and P2 proteins constitute the stalk. All these extending proteins, that have a high degree of flexibility due to a hinge between their N- and C-terminal
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RecA kinetically selects homologous DNA by testing a five- or six-nucleotide matching sequence and deforming the second DNA Q. Rev. Biophys. (IF 6.1) Pub Date : 2018-12-17 Masayuki Takahashi
RecA family proteins pair two DNAs with the same sequence to promote strand exchange during homologous recombination. To understand how RecA proteins search for and recognize homology, we sought to determine the length of homologous sequence that permits RecA to start its reaction. Specifically, we analyzed the effect of sequence heterogeneity on the association rate of homologous DNA with RecA/single-stranded
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Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design Q. Rev. Biophys. (IF 6.1) Pub Date : 2018-11-26 Vaida Linkuvienė, Asta Zubrienė, Elena Manakova, Vytautas Petrauskas, Lina Baranauskienė, Audrius Zakšauskas, Alexey Smirnov, Saulius Gražulis, John E. Ladbury, Daumantas Matulis
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Key role of the REC lobe during CRISPR–Cas9 activation by ‘sensing’, ‘regulating’, and ‘locking’ the catalytic HNH domain Q. Rev. Biophys. (IF 6.1) Pub Date : 2018-08-05 Giulia Palermo, Janice S. Chen, Clarisse G. Ricci, Ivan Rivalta, Martin Jinek, Victor S. Batista, Jennifer A. Doudna, J. Andrew McCammon