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Quarterly Reviews of Biophysics

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https://www.readbyqxmd.com/read/27660069/molecular-mechanisms-of-xeroderma-pigmentosum-xp-proteins
#1
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
#2
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
#3
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
https://www.readbyqxmd.com/read/27659286/nuclear-magnetic-resonance-nmr-applied-to-membrane-protein-complexes
#4
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, isotope-labeling and reconstitution protocols. We review approaches to deal with spectral complexity and limited spectral spectroscopic sensitivity that are usually encountered in NMR-based studies of MPCs...
January 2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/27659174/-photosystem-ii-the-water-splitting-enzyme-of-photosynthesis-and-the-origin-of-oxygen-in-our-atmosphere
#5
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 dioxide into the organic molecules of life while at the same time produced oxygen to transform our planetary atmosphere from an anaerobic to an aerobic state...
January 2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/27659043/the-evidence-for-open-and-closed-exocytosis-as-the-primary-release-mechanism
#6
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 to occur through full distention of the vesicle membrane, hence assuming exocytosis to be all or none. In contrast to the all or none hypothesis, here we discuss the evidence that during exocytosis the vesicle-membrane pore opens to release only a portion of the transmitter content during exocytosis and then close again...
January 2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/27658939/bridging-the-gap-between-in-vitro-and-in-vivo-rna-folding
#7
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 that RNA is involved in many essential cellular processes, it is critical to understand how it folds and functions in vivo...
January 2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/27658821/single-particle-electron-cryomicroscopy-trends-issues-and-future-perspective
#8
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 quantum efficiency than available previously, and to the improvement of the computational algorithms for image processing...
January 2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/27658712/the-molecular-choreography-of-protein-synthesis-translational-control-regulation-and-pathways
#9
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 translation. However, translation may not proceed linearly through a single mechanistic pathway, but likely involves multiple pathways and branchpoints...
January 2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/27658613/thermal-protein-unfolding-by-differential-scanning-calorimetry-and-circular-dichroism-spectroscopy-two-state-model-versus-sequential-unfolding
#10
Joachim Seelig, Hans-Joachim Schönfeld
Thermally-induced protein unfolding is commonly described with the two-state model. This model assumes only two types of protein molecules in solution, the native (N) and the denatured, unfolded (U) protein. In reality, protein unfolding is a multistep process, even if intermediate states are only sparsely populated. As an alternative approach we explore the Zimm-Bragg theory, originally developed for the α-helix-to-random coil transition of synthetic polypeptides. The theory includes intermediate structures with concentrations determined by the cooperativity of the unfolding reaction...
January 2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/27658373/qrb-discovery-introducing-original-research-to-qrb
#11
Bengt Nordén
No abstract text is available yet for this article.
January 2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/27266715/rna-structure-through-multidimensional-chemical-mapping
#12
Siqi Tian, Rhiju Das
The discoveries of myriad non-coding RNA molecules, each transiting through multiple flexible states in cells or virions, present major challenges for structure determination. Advances in high-throughput chemical mapping give new routes for characterizing entire transcriptomes in vivo, but the resulting one-dimensional data generally remain too information-poor to allow accurate de novo structure determination. Multidimensional chemical mapping (MCM) methods seek to address this challenge. Mutate-and-map (M2), RNA interaction groups by mutational profiling (RING-MaP and MaP-2D analysis) and multiplexed •OH cleavage analysis (MOHCA) measure how the chemical reactivities of every nucleotide in an RNA molecule change in response to modifications at every other nucleotide...
January 2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/27088887/protein-dynamics-and-function-from-solution-state-nmr-spectroscopy
#13
Michael Kovermann, Per Rogne, Magnus Wolf-Watz
It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis...
2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/26821792/modeling-and-simulation-of-protein-surface-interactions-achievements-and-challenges
#14
Musa Ozboyaci, Daria B Kokh, Stefano Corni, Rebecca C Wade
Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption...
2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/26347403/structural-basis-underlying-cac-rna-recognition-by-the-rrm-domain-of-dimeric-rna-binding-protein-rbpms
#15
Marianna Teplova, Thalia A Farazi, Thomas Tuschl, Dinshaw J Patel
RNA-binding protein with multiple splicing (designated RBPMS) is a higher vertebrate mRNA-binding protein containing a single RNA recognition motif (RRM). RBPMS has been shown to be involved in mRNA transport, localization and stability, with key roles in axon guidance, smooth muscle plasticity, as well as regulation of cancer cell proliferation and migration. We report on structure-function studies of the RRM domain of RBPMS bound to a CAC-containing single-stranded RNA. These results provide insights into potential topologies of complexes formed by the RBPMS RRM domain and the tandem CAC repeat binding sites as detected by photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation...
January 2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/26537408/accelerated-molecular-dynamics-simulations-of-ligand-binding-to-a-muscarinic-g-protein-coupled-receptor
#16
REVIEW
Kalli Kappel, Yinglong Miao, J Andrew McCammon
Elucidating the detailed process of ligand binding to a receptor is pharmaceutically important for identifying druggable binding sites. With the ability to provide atomistic detail, computational methods are well poised to study these processes. Here, accelerated molecular dynamics (aMD) is proposed to simulate processes of ligand binding to a G-protein-coupled receptor (GPCR), in this case the M3 muscarinic receptor, which is a target for treating many human diseases, including cancer, diabetes and obesity...
November 2015: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/26537407/unresolved-questions-in-human-copper-pump-mechanisms
#17
REVIEW
Pernilla Wittung-Stafshede
Copper (Cu) is an essential transition metal providing activity to key enzymes in the human body. To regulate the levels and avoid toxicity, cells have developed elaborate systems for loading these enzymes with Cu. Most Cu-dependent enzymes obtain the metal from the membrane-bound Cu pumps ATP7A/B in the Golgi network. ATP7A/B receives Cu from the cytoplasmic Cu chaperone Atox1 that acts as the cytoplasmic shuttle between the cell membrane Cu importer, Ctr1 and ATP7A/B. Biological, genetic and structural efforts have provided a tremendous amount of information for how the proteins in this pathway work...
November 2015: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/26537406/chromatin-remodeling-and-the-initiation-of-transcription
#18
REVIEW
Yahli Lorch, Roger D Kornberg
The nucleosome serves as a general gene repressor by the occlusion of regulatory and promoter DNA sequences. Repression is relieved by the SWI/SNF-RSC family of chromatin-remodeling complexes. Research reviewed here has revealed the essential features of the remodeling process.
November 2015: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/26537405/a-sequence-specific-dna-binding-small-molecule-triggers-the-release-of-immunogenic-signals-and-phagocytosis-in-a-model-of-b-cell-lymphoma
#19
REVIEW
JeenJoo S Kang, Peter B Dervan
Means to cause an immunogenic cell death could lead to significant insight into how cancer escapes immune control. In this study, we screened a library of five pyrrole-imidazole polyamides coding for different DNA sequences in a model of B-cell lymphoma for the upregulation of surface calreticulin, a pro-phagocytosis signal implicated in immunogenic cell death. We found that hairpin polyamide 1 triggers the release of the damage-associated molecular patterns calreticulin, ATP and HMGB1 in a slow necrotic-type cell death...
November 2015: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/26537404/a-twisting-story-how-a-single-gene-twists-a-snail-mechanogenetics
#20
REVIEW
Reiko Kuroda
Left-right (l-r) symmetry breaking and the establishment of asymmetric animal body plan during embryonic development are fundamental questions in nature. The molecular basis of l-r symmetry breaking of snails is a fascinating topic as it is determined by a maternal single handedness-determining locus at a very early developmental stage. This perspective describes the current state of the art of the chiromorphogenesis, mainly based on our own work, i.e. the first step of l-r symmetry breaking, as proven by our "Mechanogenetics", before the start of zygotic gene expression, transfer of chirality information to the cell-fate determining stage, and the expression of nodal at the blastula stage...
November 2015: Quarterly Reviews of Biophysics
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