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Biophysical Reviews

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https://www.readbyqxmd.com/read/27942270/the-dynamic-interplay-between-dna-topoisomerases-and-dna-topology
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/26998172/best-practice-biobanking-of-human-heart-tissue
#14
Sean Lal, Amy Li, David Allen, Paul D Allen, Paul Bannon, Tim Cartmill, Roger Cooke, Alan Farnsworth, Anne Keogh, Cristobal Dos Remedios
This review provides a guide to researchers who wish to establish a biobank. It also gives practical advice to investigators seeking access to samples of healthy or diseased human hearts. We begin with a brief history of the Sydney Heart Bank (SHB) from when it began in 1989, including the pivotal role played by the late Victor Chang. We discuss our standard operating procedures for tissue collection which include cryopreservation and the quality assurance needed to maintain the long-term molecular and cellular integrity of the samples...
December 2015: Biophysical Reviews
https://www.readbyqxmd.com/read/26495045/investigating-dynamic-interdomain-allostery-in-pin1
#15
Jeffrey W Peng
Signaling proteins often sequester complementary functional sites in separate domains. How do the different domains communicate with one another? An attractive system to address this question is the mitotic regulator, human Pin1 (Lu et al. 1996). Pin-1 consists of two tethered domains: a WW domain for substrate binding, and a catalytic domain for peptidyl-prolyl isomerase (PPIase) activity. Pin1 accelerates the cis-trans isomerization of phospho-Ser/Thr-Pro (pS/T-P) motifs within proteins regulating the cell cycle and neuronal development...
June 1, 2015: Biophysical Reviews
https://www.readbyqxmd.com/read/26236405/some-dis-assembly-required-partial-unfolding-in-the-par-6-allosteric-switch
#16
Dustin S Whitney, Brian F Volkman
Allostery is commonly described as a functional connection between two distant sites in a protein, where a binding event at one site alters affinity at the other. Here we review the conformational dynamics that encode an allosteric switch in the PDZ domain of Par-6. Par-6 is a scaffold protein that organizes other proteins into a complex required to initiate and maintain cell polarity. NMR measurements revealed that the PDZ domain samples an evolutionarily conserved unfolding intermediate allowing rearrangement of two adjacent loop residues that control ligand binding affinity...
June 1, 2015: Biophysical Reviews
https://www.readbyqxmd.com/read/26097522/discovery-of-allostery-in-pka-signaling
#17
Ping Zhang, Alexandr P Kornev, Jian Wu, Susan S Taylor
cAMP-dependent protein kinase (PKA) was the second protein kinase to be discovered and the PKA catalytic (C) subunit serves as a prototype for the large protein kinase superfamily that contains over 500 gene products. The protein kinases regulate much of biology in eukaryotic cells and they are now also a major therapeutic target. Although PKA was discovered nearly 50 years ago and the subsequent discovery of the regulatory subunits that bind cAMP and release the catalytic activity from the holoenzyme followed quickly...
June 1, 2015: Biophysical Reviews
https://www.readbyqxmd.com/read/26005503/nanoscale-protein-domain-motion-and-long-range-allostery-in-signaling-proteins-a-view-from-neutron-spin-echo-sprectroscopy
#18
David J E Callaway, Zimei Bu
Many cellular proteins are multi-domain proteins. Coupled domain-domain interactions in these multidomain proteins are important for the allosteric relay of signals in the cellular signaling networks. We have initiated the application of neutron spin echo spectroscopy to the study of nanoscale protein domain motions on submicrosecond time scales and on nanometer length scale. Our NSE experiments reveal the activation of protein domain motions over a long distance of over more than 100 Å in a multidomain scaffolding protein NHERF1 upon binding to another protein Ezrin...
June 2015: Biophysical Reviews
https://www.readbyqxmd.com/read/25774229/phospholamban-phosphorylation-mutation-and-structural-dynamics-a-biophysical-approach-to-understanding-and-treating-cardiomyopathy
#19
Naa-Adjeley D Ablorh, David D Thomas
We review the recent development of novel biochemical and spectroscopic methods to determine the site-specific phosphorylation, expression, mutation, and structural dynamics of phospholamban (PLB), in relation to its function (inhibition of the cardiac calcium pump, SERCA2a), with specific focus on cardiac physiology, pathology, and therapy. In the cardiomyocyte, SERCA2a actively transports Ca(2+) into the sarcoplasmic reticulum (SR) during relaxation (diastole) to create the concentration gradient that drives the passive efflux of Ca(2+) required for cardiac contraction (systole)...
March 1, 2015: Biophysical Reviews
https://www.readbyqxmd.com/read/26000062/global-low-frequency-motions-in-protein-allostery-cap-as-a-model-system
#20
Philip D Townsend, Thomas L Rodgers, Ehmke Pohl, Mark R Wilson, Tom C B McLeish, Martin J Cann
Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distant site. There is considerable evidence that allosteric cooperativity can be communicated by the modulation of protein dynamics without conformational change. The Catabolite Activator Protein (CAP) of Escherichia coli is an important experimental exemplar for entropically driven allostery. Here we discuss recent experimentally supported theoretical analysis that highlights the role of global low-frequency dynamics in allostery in CAP and identify how allostery arises as a natural consequence of changes in global low-frequency protein fluctuations on ligand binding...
2015: Biophysical Reviews
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