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Quarterly Reviews of Biophysics

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https://read.qxmd.com/read/30912495/annealing-of-ssdna-and-compaction-of-dsdna-by-the-hiv-1-nucleocapsid-and-gag-proteins-visualized-using-nanofluidic-channels
#1
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 stable conformation of NAs. Here, we explore the balance between these activities for NC and Gag by confining DNA-protein complexes in nanochannels...
January 2019: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/30670110/oxygenic-photosynthesis-history-status-and-perspective
#2
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 and theoretical techniques. Driven by sunlight photosystem II oxidizes the catalyst of water oxidation, a hetero-metallic Mn4CaO5(H2O)4 cluster...
January 2019: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/30912496/solid-and-fluid-segments-within-the-same-molecule-of-stratum-corneum-ceramide-lipid
#3
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 and molecular dynamics of the fluid lipid fraction in SC model lipids, focusing on the role of the essential SC lipid CER EOS, which is a ceramide esterified omega-hydroxy sphingosine linoleate with very long chain...
January 2018: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/30912494/folding-of-copper-proteins-role-of-the-metal
#4
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 incorporated into proteins requires descriptions of chemical, thermodynamic, kinetic and structural parameters involved in the formation of protein-metal complexes...
January 2018: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/30912493/copper-chaperone-blocks-amyloid-formation-via-ternary-complex
#5
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 in vitro. Copper ions are not freely available in the cellular environment, but when provided by Atox1, the resulting copper-dependent ternary complex blocks αS aggregation...
January 2018: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/30912492/reca-kinetically-selects-homologous-dna-by-testing-a-five-or-six-nucleotide-matching-sequence-and-deforming-the-second-dna
#6
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 DNA complex. We assumed that the reaction can start with equal likelihood at any point in the DNA, and that sequence heterogeneity abolishes some possible initiation sites...
January 2018: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/30912491/former-qrb-editor-richard-henderson-awarded-the-nobel-prize
#7
Bengt Nordén, David Lilley
No abstract text is available yet for this article.
January 2018: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/30912490/the-kink-turn-in-the-structural-biology-of-rna
#8
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 acceptors for one of these divides the k-turns into two conformational classes N3 and N1. The base pair that follows the G:A pairs (3b:3n) determines which conformation is adopted by a given k-turn...
January 2018: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/30912489/key-role-of-the-rec-lobe-during-crispr-cas9-activation-by-sensing-regulating-and-locking-the-catalytic-hnh-domain
#9
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 of the endonuclease Cas9 toward DNA cleavage. Over the unbiased simulation, we observe that the spontaneous approach of the catalytic domain HNH to the DNA cleavage site is accompanied by a remarkable structural remodeling of the recognition (REC) lobe, which exerts a key role for DNA cleavage...
January 2018: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/30912488/the-enigmatic-ribosomal-stalk
#10
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 parts, are essential for proper functionalization of some of the translation factors. The role of the stalk proteins has remained enigmatic for decades but is gradually approaching an understanding...
January 2018: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/30912486/thermodynamic-kinetic-and-structural-parameterization-of-human-carbonic-anhydrase-interactions-toward-enhanced-inhibitor-design
#11
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 are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations...
January 2018: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/30912485/anticipating-innovations-in-structural-biology
#12
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.
January 2018: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/30555184/key-role-of-the-rec-lobe-during-crispr-cas9-activation-by-sensing-regulating-and-locking-the-catalytic-hnh-domain
#13
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 of the endonuclease Cas9 toward DNA cleavage. Over the unbiased simulation, we observe that the spontaneous approach of the catalytic domain HNH to the DNA cleavage site is accompanied by a remarkable structural remodeling of the recognition (REC) lobe, which exerts a key role for DNA cleavage...
2018: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/29310726/dna-partitions-into-triplets-under-tension-in-the-presence-of-organic-cations-with-sequence-evolutionary-age-predicting-the-stability-of-the-triplet-phase-corrigendum
#14
Amirhossein Taghavi, Paul van der Schoot, Joshua T Berryman
No abstract text is available yet for this article.
January 2018: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/29233227/dna-partitions-into-triplets-under-tension-in-the-presence-of-organic-cations-with-sequence-evolutionary-age-predicting-the-stability-of-the-triplet-phase
#15
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. Considering the partitioning of the duplexes into triplets of base pairs as the first step of operation of recombinase enzymes like RecA, we emphasise the structure-function relationship in Σ DNA...
January 2017: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/29233226/what-can-be-learned-about-the-enzyme-atpase-from-single-molecule-studies-of-its-subunit-f1
#16
REVIEW
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.
January 2017: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/29233225/photosynthetic-water-splitting-by-the-mn4ca2-ox-catalyst-of-photosystem-ii-its-structure-robustness-and-mechanism
#17
REVIEW
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. This is accomplished by the relatively low energy content of four photons of visible light. PSII is a large multi-subunit membrane protein complex embedded in the lipid environment of the thylakoid membranes of plants, algae and cyanobacteria...
January 2017: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/29233224/ribosome-structural-dynamics-in-translocation-yet-another-functional-role-for-ribosomal-rna
#18
REVIEW
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 of protein synthesis. In recent years, the results of structural, biophysical and biochemical studies have provided extensive evidence that translocation is based on the structural dynamics of the ribosome itself...
January 2017: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/29233223/a-stretched-conformation-of-dna-with-a-biological-role
#19
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. Intriguingly, the same degree of extension is also found in DNA complexes with recombinase proteins, such as bacterial RecA and eukaryotic Rad51...
January 2017: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/29233222/understanding-membrane-active-antimicrobial-peptides
#20
REVIEW
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 basis for the study of membrane-active antimicrobial agents. These peptides are cationic and amphipathic, spontaneously binding to bacterial membranes and inducing transmembrane permeability to small molecules...
January 2017: Quarterly Reviews of Biophysics
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