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Biophysical Reviews

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https://www.readbyqxmd.com/read/28424742/fret-from-single-to-multiplexed-signaling-events
#1
REVIEW
Gertrude Bunt, Fred S Wouters
Förster resonance energy transfer (FRET) is a powerful tool for the visualization of molecular signaling events such as protein activities and interactions in cells. In its different implementations, FRET microscopy has been mainly used for monitoring single events. Recently, there has been a trend of extending FRET imaging towards the simultaneous detection of multiple events and interactions. The concomitant increase in experimental complexity requires a deeper understanding of the biophysical background of FRET...
April 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28424741/catalytic-robustness-and-torque-generation-of-the-f1-atpase
#2
REVIEW
Hiroyuki Noji, Hiroshi Ueno, Duncan G G McMillan
The F1-ATPase is the catalytic portion of the FoF1 ATP synthase and acts as a rotary molecular motor when it hydrolyzes ATP. Two decades have passed since the single-molecule rotation assay of F1-ATPase was established. Although several fundamental issues remain elusive, basic properties of F-type ATPases as motor proteins have been well characterized, and a large part of the reaction scheme has been revealed by the combination of extensive structural, biochemical, biophysical, and theoretical studies. This review is intended to provide a concise summary of the fundamental features of F1-ATPases, by use of the well-described model F1 from the thermophilic Bacillus PS3 (TF1)...
April 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28424740/essential-role-of-long-non-coding-rnas-in-de-novo-chromatin-modifications-the-genomic-address-code-hypothesis
#3
Ken Nishikawa, Akira R Kinjo
The epigenome, i.e., the whole of chromatin modifications, is transferred from mother to daughter cells during cell differentiation. When de novo chromatin modifications (establishment or erasure of, respectively, new or pre-existing DNA methylations and/or histone modifications) are made in a daughter cell, however, it has a different epigenome than its mother cell. Although de novo chromatin modification is an important event that comprises elementary processes of cell differentiation, its molecular mechanism remains poorly understood...
April 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28303166/single-molecule-studies-of-high-mobility-group-b-architectural-dna-bending-proteins
#4
REVIEW
Divakaran Murugesapillai, Micah J McCauley, L James Maher, Mark C Williams
Protein-DNA interactions can be characterized and quantified using single molecule methods such as optical tweezers, magnetic tweezers, atomic force microscopy, and fluorescence imaging. In this review, we discuss studies that characterize the binding of high-mobility group B (HMGB) architectural proteins to single DNA molecules. We show how these studies are able to extract quantitative information regarding equilibrium binding as well as non-equilibrium binding kinetics. HMGB proteins play critical but poorly understood roles in cellular function...
February 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28203306/accounting-for-thermodynamic-non-ideality-in-the-guinier-region-of-small-angle-scattering-data-of-proteins
#5
David J Scott
Hydrodynamic studies of the solution properties of proteins and other biological macromolecules are often hard to interpret when the sample is present at a reasonably concentrated solution. The reason for this is that solutions exhibit deviations from ideal behaviour which is manifested as thermodynamic non-ideality. The range of concentrations at which this behaviour typically is exhibited is as low as 1-2 mg/ml, well within the range of concentrations used for their analysis by techniques such as small-angle scattering...
December 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28275417/dna-supercoiling-during-transcription
#6
Jie Ma, Michelle D Wang
The twin-supercoiled-domain model describes how transcription can drive DNA supercoiling, and how DNA supercoiling, in turn plays an important role in regulating gene transcription. In vivo and in vitro experiments have disclosed many details of the complex interactions in this relationship, and recently new insights have been gained with the help of genome-wide DNA supercoiling mapping techniques and single molecule methods. This review summarizes the general mechanisms of the interplay between DNA supercoiling and transcription, considers the biological implications, and focuses on recent important discoveries and technical advances in this field...
November 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28133491/insights-into-genome-architecture-deduced-from-the-properties-of-short-lac-repressor-mediated-dna-loops
#7
Pamela J Perez, Wilma K Olson
Genomic DNA is vastly longer than the space allotted to it in a cell. The molecule must fold with a level of organization that satisfies the imposed spatial constraints as well as allows for the processing of genetic information. Key players in this organization include the negative supercoiling of DNA, which facilitates the unwinding of the double-helical molecule, and the associations of DNA with proteins, which partition the DNA into isolated loops, or domains. In order to gain insight into the principles of genome organization and to visualize the folding of spatially constrained DNA, we have developed new computational methods to identify the preferred three-dimensional pathways of protein-mediated DNA loops and to characterize the topological properties of these structures...
November 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/27942270/the-dynamic-interplay-between-dna-topoisomerases-and-dna-topology
#8
Yeonee Seol, Keir C Neuman
Topological properties of DNA influence its structure and biochemical interactions. Within the cell DNA topology is constantly in flux. Transcription and other essential processes including DNA replication and repair, alter the topology of the genome, while introducing additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome...
September 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/27551324/protein-dna-and-ion-dna-interactions-revealed-through-contrast-variation-saxs
#9
Joshua M Tokuda, Suzette A Pabit, Lois Pollack
Understanding how DNA carries out its biological roles requires knowledge of its interactions with biological partners. Since DNA is a polyanionic polymer, electrostatic interactions contribute significantly. These interactions are mediated by positively charged protein residues or charge compensating cations. Direct detection of these partners and/or their effect on DNA conformation poses challenges, especially for monitoring conformational dynamics in real time. Small-angle x-ray scattering (SAXS) is uniquely sensitive to both the conformation and local environment (i...
June 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28058066/recent-insights-from-in-vitro-single-molecule-studies-into-nucleosome-structure-and-dynamics
#10
REVIEW
Orkide Ordu, Alexandra Lusser, Nynke H Dekker
Eukaryotic DNA is tightly packed into a hierarchically ordered structure called chromatin in order to fit into the micron-scaled nucleus. The basic unit of chromatin is the nucleosome, which consists of a short piece of DNA wrapped around a core of eight histone proteins. In addition to their role in packaging DNA, nucleosomes impact the regulation of essential nuclear processes such as replication, transcription, and repair by controlling the accessibility of DNA. Thus, knowledge of this fundamental DNA-protein complex is crucial for understanding the mechanisms of gene control...
2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28035245/protein-dna-interactions-in-complex-dna-topologies-expect-the-unexpected
#11
REVIEW
Agnes Noy, Thana Sutthibutpong, Sarah A Harris
DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature...
2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28035244/effects-of-dna-supercoiling-on-chromatin-architecture
#12
REVIEW
Samuel Corless, Nick Gilbert
Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of kilobases in size. RNA polymerase is a powerful motor which, prevented from turning with the tight helical pitch of the DNA, generates over-wound DNA ahead of itself and under-wound DNA behind. Mounting evidence supports a central role for transcription-dependent DNA supercoiling in disrupting chromatin structure at all scales...
2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28003859/measurement-of-amyloid-formation-by-turbidity-assay-seeing-through-the-cloud
#13
REVIEW
Ran Zhao, Masatomo So, Hendrik Maat, Nicholas J Ray, Fumio Arisaka, Yuji Goto, John A Carver, Damien Hall
Detection of amyloid growth is commonly carried out by measurement of solution turbidity, a low-cost assay procedure based on the intrinsic light scattering properties of the protein aggregate. Here, we review the biophysical chemistry associated with the turbidimetric assay methodology, exploring the reviewed literature using a series of pedagogical kinetic simulations. In turn, these simulations are used to interrogate the literature concerned with in vitro drug screening and the assessment of amyloid aggregation mechanisms...
2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28003858/analytical-methods-for-structural-ensembles-and-dynamics-of-intrinsically-disordered-proteins
#14
REVIEW
Marieke Schor, Antonia S J S Mey, Cait E MacPhee
Intrinsically disordered proteins, proteins that do not have a well-defined three-dimensional structure, make up a significant proportion of our proteome and are particularly prevalent in signaling and regulation. Although their importance has been realized for two decades, there is a lack of high-resolution experimental data. Molecular dynamics simulations have been crucial in reaching our current understanding of the dynamical structural ensemble sampled by intrinsically disordered proteins. In this review, we discuss enhanced sampling simulation methods that are particularly suitable to characterize the structural ensemble, along with examples of applications and limitations...
2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28003857/assessing-sedimentation-equilibrium-profiles-in-analytical-ultracentrifugation-experiments-on-macromolecules-from-simple-average-molecular-weight-analysis-to-molecular-weight-distribution-and-interaction-analysis
#15
REVIEW
Stephen E Harding, Richard B Gillis, Gary G Adams
Molecular weights (molar masses), molecular weight distributions, dissociation constants and other interaction parameters are fundamental characteristics of proteins, nucleic acids, polysaccharides and glycoconjugates in solution. Sedimentation equilibrium analytical ultracentrifugation provides a powerful method with no supplementary immobilization, columns or membranes required. It is a particularly powerful tool when used in conjunction with its sister technique, namely sedimentation velocity. Here, we describe key approaches now available and their application to the characterization of antibodies, polysaccharides and glycoconjugates...
2016: Biophysical Reviews
https://www.readbyqxmd.com/read/27738453/effects-of-dna-supercoiling-on-chromatin-architecture
#16
REVIEW
Samuel Corless, Nick Gilbert
Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of kilobases in size. RNA polymerase is a powerful motor which, prevented from turning with the tight helical pitch of the DNA, generates over-wound DNA ahead of itself and under-wound DNA behind. Mounting evidence supports a central role for transcription-dependent DNA supercoiling in disrupting chromatin structure at all scales...
2016: Biophysical Reviews
https://www.readbyqxmd.com/read/27738452/protein-dna-interactions-in-complex-dna-topologies-expect-the-unexpected
#17
REVIEW
Agnes Noy, Thana Sutthibutpong, Sarah A Harris
DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature...
2016: Biophysical Reviews
https://www.readbyqxmd.com/read/27279920/uv-vis-spectroscopy-of-tyrosine-side-groups-in-studies-of-protein-structure-part-2-selected-applications
#18
Jan M Antosiewicz, David Shugar
In Part 2 we discuss application of several different types of UV-Vis spectroscopy, such as normal, difference, and second-derivative UV absorption spectroscopy, fluorescence spectroscopy, linear and circular dichroism spectroscopy, and Raman spectroscopy, of the side-chain of tyrosine residues in different molecular environments. We review the ways these spectroscopies can be used to probe complex protein structures.
2016: Biophysical Reviews
https://www.readbyqxmd.com/read/27279919/uv-vis-spectroscopy-of-tyrosine-side-groups-in-studies-of-protein-structure-part-1-basic-principles-and-properties-of-tyrosine-chromophore
#19
Jan M Antosiewicz, David Shugar
Spectroscopic properties of tyrosine residues may be employed in structural studies of proteins. Here we discuss several different types of UV-Vis spectroscopy, like normal, difference and second-derivative UV absorption spectroscopy, fluorescence spectroscopy, linear and circular dichroism spectroscopy, and Raman spectroscopy, and corresponding optical properties of the tyrosine chromophore, phenol, which are used to study protein structure.
2016: Biophysical Reviews
https://www.readbyqxmd.com/read/27279918/design-and-development-of-genetically-encoded-fluorescent-sensors-to-monitor-intracellular-chemical-and-physical-parameters
#20
Arno Germond, Hideaki Fujita, Taro Ichimura, Tomonobu M Watanabe
Over the past decades many researchers have made major contributions towards the development of genetically encoded (GE) fluorescent sensors derived from fluorescent proteins. GE sensors are now used to study biological phenomena by facilitating the measurement of biochemical behaviors at various scales, ranging from single molecules to single cells or even whole animals. Here, we review the historical development of GE fluorescent sensors and report on their current status. We specifically focus on the development strategies of the GE sensors used for measuring pH, ion concentrations (e...
2016: Biophysical Reviews
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