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Quarterly Reviews of Biophysics

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https://www.readbyqxmd.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
#1
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://www.readbyqxmd.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
#2
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://www.readbyqxmd.com/read/29233226/what-can-be-learned-about-the-enzyme-atpase-from-single-molecule-studies-of-its-subunit-f1
#3
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://www.readbyqxmd.com/read/29233225/photosynthetic-water-splitting-by-the-mn4ca2-ox-catalyst-of-photosystem-ii-its-structure-robustness-and-mechanism
#4
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://www.readbyqxmd.com/read/29233224/ribosome-structural-dynamics-in-translocation-yet-another-functional-role-for-ribosomal-rna
#5
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://www.readbyqxmd.com/read/29233223/a-stretched-conformation-of-dna-with-a-biological-role
#6
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://www.readbyqxmd.com/read/29233222/understanding-membrane-active-antimicrobial-peptides
#7
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
https://www.readbyqxmd.com/read/29233221/lysozyme-s-lectin-like-characteristics-facilitates-its-immune-defense-function
#8
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. pH-dependent structural rearrangements of HL after interaction with the disaccharide were observed through nuclear magnetic resonance...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/29233220/a-new-paradigm-for-atomically-detailed-simulations-of-kinetics-in-biophysical-systems
#9
REVIEW
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, simulations at biological time scales are challenging. Typical computer resources are insufficient to provide the ensemble of trajectories at the correct length that is required for straightforward calculations of time scales...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/29233219/a-molecular-engineering-toolbox-for-the-structural-biologist
#10
REVIEW
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 the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/29233218/secondary-nucleation-of-monomers-on-fibril-surface-dominates-%C3%AE-synuclein-aggregation-and-provides-autocatalytic-amyloid-amplification
#11
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 the aggregation rate on monomer concentration. The molecular mechanism underlying this process could be nucleation of monomers on fibril surfaces or fibril fragmentation...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/29233217/chromatin-remodeling-for-transcription
#12
REVIEW
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 complexes for transcription. RSC creates a nucleosome-free region in front of a gene, flanked by strongly positioned +1 and -1 nucleosomes, with the transcription start site typically 10-15 bp inside the border of the +1 nucleosome...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/29233216/nucleic-acids-function-and-potential-for-abiogenesis
#13
REVIEW
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, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/29233215/unraveling-amyloid-formation-paths-of-parkinson-s-disease-protein-%C3%AE-synuclein-triggered-by-anionic-vesicles
#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 charged vesicles of DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, sodium salt) and DOPG (1,2-dioleoyl-sn-glycero-3-phospho-(1'-rac-glycerol), sodium salt) and the consequences of such interactions on αS amyloid formation...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/29233214/microdroplet-fusion-mass-spectrometry-accelerated-kinetics-of-acid-induced-chlorophyll-demetallation
#15
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 the traveling distance of the fused microdroplets between the fusion region and the inlet of a mass spectrometer...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/28093096/structural-biology-of-supramolecular-assemblies-by-magic-angle-spinning-nmr-spectroscopy
#16
REVIEW
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 detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/28100928/mass-spectrometry-a-technique-of-many-faces
#17
REVIEW
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 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 approaches provides unprecedented information on multiple levels. We demonstrate this on the ubiquitin-proteasome proteolytic pathway, a process that is responsible for protein turnover...
January 2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/27660069/molecular-mechanisms-of-xeroderma-pigmentosum-xp-proteins
#18
Sandra C Koch, Nina Simon, Charlotte Ebert, Thomas Carell
Nucleotide excision repair (NER) is a highly versatile and efficient DNA repair process, which is responsible for the removal of a large number of structurally diverse DNA lesions. Its extreme broad substrate specificity ranges from DNA damages formed upon exposure to ultraviolet radiation to numerous bulky DNA adducts induced by mutagenic environmental chemicals and cytotoxic drugs used in chemotherapy. Defective NER leads to serious diseases, such as xeroderma pigmentosum (XP). Eight XP complementation groups are known of which seven (XPA-XPG) are caused by mutations in genes involved in the NER process...
January 2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/27659610/photosystem-ii-the-water-splitting-enzyme-of-photosynthesis-and-the-origin-of-oxygen-in-our-atmosphere-corrigendum
#19
James Barber
No abstract text is available yet for this article.
January 2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/27659445/quantum-entanglement-facts-and-fiction-how-wrong-was-einstein-after-all
#20
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 are important in many biophysical contexts and involve coupling between subsystems in which virtual excitations lead to eigenstates of the total Hamiltonian, but not for the separate subsystems...
January 2016: Quarterly Reviews of Biophysics
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