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Macromolecular room temperature crystallography Q. Rev. Biophys. (IF 5.545) 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 5.545) 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 Q. Rev. Biophys. (IF 5.545) 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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Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives Q. Rev. Biophys. (IF 5.545) 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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Exploring the dynamics of flagellar dynein within the axoneme with Fluctuating Finite Element Analysis. Q. Rev. Biophys. (IF 5.545) 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 5.545) 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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Biophysical studies of protein misfolding and aggregation in in vivo models of Alzheimer's and Parkinson's diseases. Q. Rev. Biophys. (IF 5.545) 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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Survival of the cheapest: how proteome cost minimization drives evolution. Q. Rev. Biophys. (IF 5.545) 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 5.545) 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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Anionic food color tartrazine enhances antibacterial efficacy of histatin-derived peptide DHVAR4 by fine-tuning its membrane activity. Q. Rev. Biophys. (IF 5.545) 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 5.545) 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 both in vivo and in vitro observations. The chronologue is organized into various topics of
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De novo protein design, a retrospective. Q. Rev. Biophys. (IF 5.545) 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, or de 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 5.545) Pub Date : 2020-01-31 András Láng,Imre Jákli,Kata Nóra Enyedi,Gábor Mező,Dóra K Menyhárd,András Perczel
At any –Asn/AspGly– sites in proteins a spontaneous backbone isomerization occurs within days under physiological conditions leading to various forms of proteopathy. This unwanted transformation especially harmful to long-lived proteins (e.g. hemoglobin and crystallins), can be slowed down, though never stopped, by a rigid three-dimensional protein fold, if it can delay in the conformational maze,
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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 5.545) 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 5.545) 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 5.545) 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 5.545) 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 5.545) 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. Eighteen α-chains and eight β-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
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Navigating at night: fundamental limits on the sensitivity of radical pair magnetoreception under dim light. Q. Rev. Biophys. (IF 5.545) 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 5.545) Pub Date : 2019-08-19 Robert J Trachman,Adrian R Ferré-D'Amaré
Fluorescence turn-on aptamers, in vitro evolved 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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Annealing of ssDNA and compaction of dsDNA by the HIV-1 nucleocapsid and Gag proteins visualized using nanofluidic channels. Q. Rev. Biophys. (IF 5.545) Pub Date : 2019-01-01 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 5.545) Pub Date : 2019-01-01 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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Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Q. Rev. Biophys. (IF 5.545) Pub Date : 2018-12-18 Giulia Palermo,Janice S Chen,Clarisse G Ricci,Ivan Rivalta,Martin Jinek,Victor S Batista,Jennifer A Doudna,J Andrew McCammon
Understanding the conformational dynamics of CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 is of the utmost importance for improving its genome editing capability. Here, molecular dynamics simulations performed using Anton-2 - a specialized supercomputer capturing micro-to-millisecond biophysical events in real time and at atomic-level resolution - reveal the activation process
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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 5.545) Pub Date : 2018-01-10 Amirhossein Taghavi,Paul van der Schoot,Joshua T Berryman
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Folding of copper proteins: role of the metal? Q. Rev. Biophys. (IF 5.545) Pub Date : 2018-01-01 Candan Ariöz,Pernilla Wittung-Stafshede
Copper is a redox-active transition metal ion required for the function of many essential human proteins. For biosynthesis of proteins coordinating copper, the metal may bind before, during or after folding of the polypeptide. If the metal binds to unfolded or partially folded structures of the protein, such coordination may modulate the folding reaction. The molecular understanding of how copper is
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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 5.545) Pub Date : 2018-01-01 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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The kink-turn in the structural biology of RNA. Q. Rev. Biophys. (IF 5.545) Pub Date : 2018-01-01 Lin Huang,David M J Lilley
The kink-turn (k-turn) is a widespread structural motif found in functional RNA species. It typically comprises a three-nucleotide bulge followed by tandem trans sugar edge-Hoogsteen G:A base pairs. It introduces a sharp kink into the axis of duplex RNA, juxtaposing the minor grooves. Cross-strand H-bonds form at the interface, accepted by the conserved adenine nucleobases of the G:A basepairs. Alternative
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The enigmatic ribosomal stalk. Q. Rev. Biophys. (IF 5.545) Pub Date : 2018-01-01 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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Solid and fluid segments within the same molecule of stratum corneum ceramide lipid. Q. Rev. Biophys. (IF 5.545) Pub Date : 2018-01-01 Quoc Dat Pham,Enamul H Mojumdar,Gert S Gooris,Joke A Bouwstra,Emma Sparr,Daniel Topgaard
The outer layer of the skin, stratum corneum (SC) is an efficient transport barrier and it tolerates mechanical deformation. At physiological conditions, the majority of SC lipids are solid, while the presence of a small amount of fluid lipids is considered crucial for SC barrier and material properties. Here we use solid-state and diffusion nuclear magnetic resonance to characterize the composition
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Copper chaperone blocks amyloid formation via ternary complex. Q. Rev. Biophys. (IF 5.545) Pub Date : 2018-01-01 Istvan Horvath,Tony Werner,Ranjeet Kumar,Pernilla Wittung-Stafshede
Protein misfolding in cells is avoided by a network of protein chaperones that detect misfolded or partially folded species. When proteins escape these control systems, misfolding may result in protein aggregation and amyloid formation. We here show that aggregation of the amyloidogenic protein α-synuclein (αS), the key player in Parkinson's disease, is controlled by the copper transport protein Atox1
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Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design. Q. Rev. Biophys. (IF 5.545) Pub Date : 2018-01-01 Vaida Linkuvienė,Asta Zubrienė,Elena Manakova,Vytautas Petrauskas,Lina Baranauskienė,Audrius Zakšauskas,Alexey Smirnov,Saulius Gražulis,John E Ladbury,Daumantas Matulis
The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules
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Former QRB Editor Richard Henderson awarded the Nobel Prize. Q. Rev. Biophys. (IF 5.545) Pub Date : 2018-01-01 Bengt Nordén,David Lilley
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Anticipating innovations in structural biology. Q. Rev. Biophys. (IF 5.545) Pub Date : 2018-01-01 Helen M Berman,Catherine L Lawson,Brinda Vallat,Margaret J Gabanyi
In this review, we describe how the interplay among science, technology and community interests contributed to the evolution of four structural biology data resources. We present the method by which data deposited by scientists are prepared for worldwide distribution, and argue that data archiving in a trusted repository must be an integral part of any scientific investigation.
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Secondary nucleation of monomers on fibril surface dominates α-synuclein aggregation and provides autocatalytic amyloid amplification. Q. Rev. Biophys. (IF 5.545) Pub Date : 2017-12-14 Ricardo Gaspar,Georg Meisl,Alexander K Buell,Laurence Young,Clemens F Kaminski,Tuomas P J Knowles,Emma Sparr,Sara Linse
Parkinson's disease (PD) is characterized by proteinaceous aggregates named Lewy Bodies and Lewy Neurites containing α-synuclein fibrils. The underlying aggregation mechanism of this protein is dominated by a secondary process at mildly acidic pH, as in endosomes and other organelles. This effect manifests as a strong acceleration of the aggregation in the presence of seeds and a weak dependence of
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A molecular engineering toolbox for the structural biologist. Q. Rev. Biophys. (IF 5.545) Pub Date : 2017-12-14 Galia T Debelouchina,Tom W Muir
Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into
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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. Q. Rev. Biophys. (IF 5.545) Pub Date : 2017-12-14 Amirhossein Taghavi,Paul van der Schoot,Joshua T Berryman
Using atomistic simulations, we show the formation of stable triplet structure when particular GC-rich DNA duplexes are extended in solution over a timescale of hundreds of nanoseconds, in the presence of organic salt. We present planar-stacked triplet disproportionated DNA (Σ DNA) as a possible solution phase of the double helix under tension, subject to sequence and the presence of stabilising co-factors
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What can be learned about the enzyme ATPase from single-molecule studies of its subunit F1? Q. Rev. Biophys. (IF 5.545) Pub Date : 2017-12-14 Sándor Volkán-Kacso,Rudolph A Marcus
We summarize the different types of single molecule experiments on the F1 component of FOF1-ATP Synthase and what has been learned from them. We also describe results from our recent studies on interpreting the experiments using a chemical-mechanical theory for these biological motors.
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Photosynthetic water splitting by the Mn4Ca2+OX catalyst of photosystem II: its structure, robustness and mechanism. Q. Rev. Biophys. (IF 5.545) Pub Date : 2017-12-14 James Barber
The biological energy cycle of our planet is driven by photosynthesis whereby sunlight is absorbed by chlorophyll and other accessory pigments. The excitation energy is then efficiently transferred to a reaction centre where charge separation occurs in a few picoseconds. In the case of photosystem II (PSII), the energy of the charge transfer state is used to split water into oxygen and reducing equivalents
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Ribosome structural dynamics in translocation: yet another functional role for ribosomal RNA. Q. Rev. Biophys. (IF 5.545) Pub Date : 2017-12-14 Harry F Noller,Laura Lancaster,Srividya Mohan,Jie Zhou
Ribosomes are remarkable ribonucleoprotein complexes that are responsible for protein synthesis in all forms of life. They polymerize polypeptide chains programmed by nucleotide sequences in messenger RNA in a mechanism mediated by transfer RNA. One of the most challenging problems in the ribosome field is to understand the mechanism of coupled translocation of mRNA and tRNA during the elongation phase
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A stretched conformation of DNA with a biological role? Q. Rev. Biophys. (IF 5.545) Pub Date : 2017-12-14 Niklas Bosaeus,Anna Reymer,Tamás Beke-Somfai,Tom Brown,Masayuki Takahashi,Pernilla Wittung-Stafshede,Sandra Rocha,Bengt Nordén
We have discovered a well-defined extended conformation of double-stranded DNA, which we call Σ-DNA, using laser-tweezers force-spectroscopy experiments. At a transition force corresponding to free energy change ΔG = 1·57 ± 0·12 kcal (mol base pair)-1 60 or 122 base-pair long synthetic GC-rich sequences, when pulled by the 3'-3' strands, undergo a sharp transition to the 1·52 ± 0·04 times longer Σ-DNA
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Understanding membrane-active antimicrobial peptides. Q. Rev. Biophys. (IF 5.545) Pub Date : 2017-12-14 Huey W Huang,Nicholas E Charron
Bacterial membranes represent an attractive target for the design of new antibiotics to combat widespread bacterial resistance to traditional inhibitor-based antibiotics. Understanding how antimicrobial peptides (AMPs) and other membrane-active agents attack membranes could facilitate the design of new, effective antimicrobials. AMPs, which are small, gene-encoded host defense proteins, offer a promising
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Lysozyme's lectin-like characteristics facilitates its immune defense function. Q. Rev. Biophys. (IF 5.545) Pub Date : 2017-12-14 Ruiyan Zhang,Lisha Wu,Thomas Eckert,Monika Burg-Roderfeld,Miguel A Rojas-Macias,Thomas Lütteke,Vadim B Krylov,Dmitry A Argunov,Aritreyee Datta,Philipp Markart,Andreas Guenther,Bengt Norden,Roland Schauer,Anirban Bhunia,Mushira Abdelaziz Enani,Martin Billeter,Axel J Scheidig,Nikolay E Nifantiev,Hans-Christian Siebert
Interactions between human lysozyme (HL) and the lipopolysaccharide (LPS) of Klebsiella pneumoniae O1, a causative agent of lung infection, were identified by surface plasmon resonance. To characterize the molecular mechanism of this interaction, HL binding to synthetic disaccharides and tetrasaccharides representing one and two repeating units, respectively, of the O-chain of this LPS were studied
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A new paradigm for atomically detailed simulations of kinetics in biophysical systems. Q. Rev. Biophys. (IF 5.545) Pub Date : 2017-12-14 Ron Elber
The kinetics of biochemical and biophysical events determined the course of life processes and attracted considerable interest and research. For example, modeling of biological networks and cellular responses relies on the availability of information on rate coefficients. Atomically detailed simulations hold the promise of supplementing experimental data to obtain a more complete kinetic picture. However
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Chromatin-remodeling for transcription. Q. Rev. Biophys. (IF 5.545) Pub Date : 2017-12-14 Yahli Lorch,Roger D Kornberg
The nucleosome serves as a general gene repressor, preventing all initiation of transcription except that which is brought about by specific positive regulatory mechanisms. The positive mechanisms begin with chromatin-remodeling by complexes that slide, disrupt, or otherwise alter the structure and organization of nucleosomes. RSC in yeast and its counterpart PBAF in human cells are the major remodeling
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Nucleic acids: function and potential for abiogenesis. Q. Rev. Biophys. (IF 5.545) Pub Date : 2017-12-14 Falk Wachowius,James Attwater,Philipp Holliger
The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically
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Unraveling amyloid formation paths of Parkinson's disease protein α-synuclein triggered by anionic vesicles. Q. Rev. Biophys. (IF 5.545) Pub Date : 2017-12-14 Juris Kiskis,Istvan Horvath,Pernilla Wittung-Stafshede,Sandra Rocha
Amyloid formation of the synaptic brain protein α-synuclein (αS) is related to degeneration of dopaminergic neurons in Parkinson's disease patients. αS is thought to function in vesicle transport and fusion and it binds strongly to negatively charged vesicles in vitro. Here we combined circular dichroism, fluorescence and imaging methods in vitro to characterize the interaction of αS with negatively
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Microdroplet fusion mass spectrometry: accelerated kinetics of acid-induced chlorophyll demetallation. Q. Rev. Biophys. (IF 5.545) Pub Date : 2017-12-14 Jae Kyoo Lee,Hong Gil Nam,Richard N Zare
Kinetics of acid-induced chlorophyll demetallation was recorded in microdroplets by fusing a stream of microdroplets containing 40 µM chlorophyll a or b dissolved in methanol with a stream of aqueous microdroplets containing 35 mM hydrochloric acid (pH = 1·46). The kinetics of the demetallation of chlorophyll in the fused microdroplets (14 ± 6 µm diameter; 84 ± 18 m s-1 velocity) was recorded by controlling
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Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy. Q. Rev. Biophys. (IF 5.545) Pub Date : 2017-01-18 Caitlin M Quinn,Tatyana Polenova
In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast MAS, proton
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QRB Discovery: introducing original research to QRB. Q. Rev. Biophys. (IF 5.545) Pub Date : 2016-09-24 Bengt Nordén
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Frontier methods in coherent X-ray diffraction for high-resolution structure determination Q. Rev. Biophys. (IF 5.545) Pub Date : 2016-12-12 Marcus Gallagher-Jones; Jose A. Rodriguez; Jianwei Miao
In 1912, Max von Laue and collaborators first observed diffraction spots from a millimeter-sized crystal of copper sulfate using an X-ray tube. Crystallography was born of this experiment, and since then, diffraction by both X-rays and electrons has revealed a myriad of inorganic and organic structures, including structures of complex protein assemblies. Advancements in X-ray sources have spurred a
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Spatially-controlled illumination microscopy: For prolonged live-cell and live-tissue imaging with extended dynamic range Q. Rev. Biophys. (IF 5.545) Pub Date : 2016-12-12 Venkataraman Krishnaswami; Cornelis J. F. Van Noorden; Erik M. M. Manders; Ron A. Hoebe
Live-cell and live-tissue imaging using fluorescence optical microscopes presents an inherent trade-off between image quality and photodamage. Spatially-controlled illumination microscopy (SCIM) aims to strike the right balance between obtaining good image quality and minimizing the risk of photodamage. In traditional imaging, illumination is performed with a spatially-uniform light dose resulting
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Mass Spectrometry: A Technique of Many Faces. Q. Rev. Biophys. (IF 5.545) Pub Date : 2016-11-28 Maya A Olshina,Michal Sharon
Protein complexes form the critical foundation for a wide range of biological process, however understanding the intricate details of their activities is often challenging. In this review we describe how mass spectrometry (MS) plays a key role in the analysis of protein assemblies and the cellular pathways which they are involved in. Specifically, we discuss how the versatility of mass spectrometric
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Photosystem II: the water splitting enzyme of photosynthesis and the origin of oxygen in our atmosphere - CORRIGENDUM. Q. Rev. Biophys. (IF 5.545) Pub Date : 2016-08-31 James Barber
About 3 billion years ago an enzyme emerged which would dramatically change the chemical composition of our planet and set in motion an unprecedented explosion in biological activity. This enzyme used solar energy to power the thermodynamically and chemically demanding reaction of water splitting. In so doing it provided biology with an unlimited supply of reducing equivalents needed to convert carbon
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Quantum entanglement: facts and fiction - how wrong was Einstein after all? Q. Rev. Biophys. (IF 5.545) Pub Date : 2016-08-31 Bengt Nordén
Einstein was wrong with his 1927 Solvay Conference claim that quantum mechanics is incomplete and incapable of describing diffraction of single particles. However, the Einstein-Podolsky-Rosen paradox of entangled pairs of particles remains lurking with its ‘spooky action at a distance’. In molecules quantum entanglement can be viewed as basis of both chemical bonding and excitonic states. The latter
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Nuclear magnetic resonance (NMR) applied to membrane-protein complexes. Q. Rev. Biophys. (IF 5.545) Pub Date : 2016-08-08 Mohammed Kaplan,Cecilia Pinto,Klaartje Houben,Marc Baldus
Increasing evidence suggests that most proteins occur and function in complexes rather than as isolated entities when embedded in cellular membranes. Nuclear magnetic resonance (NMR) provides increasing possibilities to study structure, dynamics and assembly of such systems. In our review, we discuss recent methodological progress to study membrane–protein complexes (MPCs) by NMR, starting with expression
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'Photosystem II: the water splitting enzyme of photosynthesis and the origin of oxygen in our atmosphere'. Q. Rev. Biophys. (IF 5.545) Pub Date : 2016-08-01 James Barber
About 3 billion years ago an enzyme emerged which would dramatically change the chemical composition of our planet and set in motion an unprecedented explosion in biological activity. This enzyme used solar energy to power the thermodynamically and chemically demanding reaction of water splitting. In so doing it provided biology with an unlimited supply of reducing equivalents needed to convert carbon
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Single particle electron cryomicroscopy: trends, issues and future perspective. Q. Rev. Biophys. (IF 5.545) Pub Date : 2016-07-22 Kutti R Vinothkumar,Richard Henderson
There has been enormous progress during the last few years in the determination of three-dimensional biological structures by single particle electron cryomicroscopy (cryoEM), allowing maps to be obtained with higher resolution and from fewer images than required previously. This is due principally to the introduction of a new type of direct electron detector that has 2- to 3-fold higher detective
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The evidence for open and closed exocytosis as the primary release mechanism. Q. Rev. Biophys. (IF 5.545) Pub Date : 2016-07-18 Lin Ren,Lisa J Mellander,Jacqueline Keighron,Ann-Sofie Cans,Michael E Kurczy,Irina Svir,Alexander Oleinick,Christian Amatore,Andrew G Ewing
Exocytosis is the fundamental process by which cells communicate with each other. The events that lead up to the fusion of a vesicle loaded with chemical messenger with the cell membrane were the subject of a Nobel Prize in 2013. However, the processes occurring after the initial formation of a fusion pore are very much still in debate. The release of chemical messenger has traditionally been thought
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Bridging the gap between in vitro and in vivo RNA folding. Q. Rev. Biophys. (IF 5.545) Pub Date : 2016-06-24 Kathleen A Leamy,Sarah M Assmann,David H Mathews,Philip C Bevilacqua
Deciphering the folding pathways and predicting the structures of complex three-dimensional biomolecules is central to elucidating biological function. RNA is single-stranded, which gives it the freedom to fold into complex secondary and tertiary structures. These structures endow RNA with the ability to perform complex chemistries and functions ranging from enzymatic activity to gene regulation. Given
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The molecular choreography of protein synthesis: translational control, regulation, and pathways. Q. Rev. Biophys. (IF 5.545) Pub Date : 2016-06-24 Jin Chen,Junhong Choi,Seán E O'Leary,Arjun Prabhakar,Alexey Petrov,Rosslyn Grosely,Elisabetta Viani Puglisi,Joseph D Puglisi
Translation of proteins by the ribosome regulates gene expression, with recent results underscoring the importance of translational control. Misregulation of translation underlies many diseases, including cancer and many genetic diseases. Decades of biochemical and structural studies have delineated many of the mechanistic details in prokaryotic translation, and sketched the outlines of eukaryotic
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