journal
https://read.qxmd.com/read/34530945/the-mechanics-of-mitotic-chromosomes
#21
JOURNAL ARTICLE
Tianlong Man, Hannes Witt, Erwin J G Peterman, Gijs J L Wuite
No abstract text is available yet for this article.
September 17, 2021: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/34225835/a-molecular-view-of-dna-flexibility
#22
JOURNAL ARTICLE
Alberto Marin-Gonzalez, J G Vilhena, Ruben Perez, Fernando Moreno-Herrero
DNA dynamics can only be understood by taking into account its complex mechanical behavior at different length scales. At the micrometer level, the mechanical properties of single DNA molecules have been well-characterized by polymer models and are commonly quantified by a persistence length of 50 nm (~150 bp). However, at the base pair level (~3.4 Å), the dynamics of DNA involves complex molecular mechanisms that are still being deciphered. Here, we review recent single-molecule experiments and molecular dynamics simulations that are providing novel insights into DNA mechanics from such a molecular perspective...
July 6, 2021: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/34165063/where-in-the-cell-is-my-protein
#23
JOURNAL ARTICLE
David J DeRosier
No abstract text is available yet for this article.
June 21, 2021: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/34003085/a-quantitative-model-of-a-cooperative-two-state-equilibrium-in-dna-experimental-tests-insights-and-predictions-corrigendum
#24
JOURNAL ARTICLE
J Michael Schurr
No abstract text is available yet for this article.
May 18, 2021: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/33785082/amphipathic-environments-for-determining-the-structure-of-membrane-proteins-by-single-particle-electron-cryo-microscopy
#25
JOURNAL ARTICLE
Christel Le Bon, Baptiste Michon, Jean-Luc Popot, Manuela Zoonens
No abstract text is available yet for this article.
March 31, 2021: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/33722316/a-quantitative-model-of-a-cooperative-two-state-equilibrium-in-dna-experimental-tests-insights-and-predictions
#26
JOURNAL ARTICLE
J Michael Schurr
Quantitative parameters for a two-state cooperative transition in duplex DNAs were finally obtained during the last 5 years. After a brief discussion of observations pertaining to the existence of the two-state equilibrium per se, the lengths, torsion, and bending elastic constants of the two states involved and the cooperativity parameter of the model are simply stated. Experimental tests of model predictions for the responses of DNA to small applied stretching, twisting, and bending stresses, and changes in temperature, ionic conditions, and sequence are described...
March 16, 2021: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/33704040/current-limitations-to-high-resolution-structure-determination-by-single-particle-cryoem
#27
JOURNAL ARTICLE
Edoardo D'Imprima, Werner Kühlbrandt
CryoEM has become the method of choice for determining the structure of large macromolecular complexes in multiple conformations, at resolutions where unambiguous atomic models can be built. Two effects that have limited progress in single-particle cryoEM are (i) beam-induced movement during image acquisition and (ii) protein adsorption and denaturation at the air-water interface during specimen preparation. While beam-induced movement now appears to have been resolved by all-gold specimen support grids with very small holes, surface effects at the air-water interface are a persistent problem...
March 11, 2021: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/33541444/hydrophobic-interactions-control-the-self-assembly-of-dna-and-cellulose
#28
JOURNAL ARTICLE
Björn Lindman, Bruno Medronho, Luís Alves, Magnus Norgren, Lars Nordenskiöld
Desoxyribosenucleic acid, DNA, and cellulose molecules self-assemble in aqueous systems. This aggregation is the basis of the important functions of these biological macromolecules. Both DNA and cellulose have significant polar and nonpolar parts and there is a delicate balance between hydrophilic and hydrophobic interactions. The hydrophilic interactions related to net charges have been thoroughly studied and are well understood. On the other hand, the detailed roles of hydrogen bonding and hydrophobic interactions have remained controversial...
February 5, 2021: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/33413726/macromolecular-room-temperature-crystallography
#29
JOURNAL ARTICLE
Marcus Fischer
X-ray crystallography enables detailed structural studies of proteins to understand and modulate their function. Conducting crystallographic experiments at cryogenic temperatures has practical benefits but potentially limits the identification of functionally important alternative protein conformations that can be revealed only at room temperature (RT). This review discusses practical aspects of preparing, acquiring, and analyzing X-ray crystallography data at RT to demystify preconceived impracticalities that freeze progress of routine RT data collection at synchrotron sources...
January 8, 2021: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/33413714/setting-up-and-operating-a-cryo-em-laboratory
#30
JOURNAL ARTICLE
Deryck J Mills
Cryo-electron microscopy (cryo-EM) has become the technique of choice for structural biology of macromolecular assemblies, after the 'resolution revolution' that has occurred in this field since 2012. With a suitable instrument, an appropriate electron detector and, last but not least, a cooperative sample it is now possible to collect images from which macromolecular structures can be determined to better than 2 Å resolution, where reliable atomic models can be built. By electron tomography and sub-tomogram averaging of cryo-samples, it is also possible to reconstruct subcellular structures to sub-nanometre resolution...
January 8, 2021: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/33298235/energy-mapping-of-the-genetic-code-and-genomic-domains-implications-for-code-evolution-and-molecular-darwinism-corrigendum
#31
JOURNAL ARTICLE
Horst H Klump, Jens Völker, Kenneth J Breslauer
No abstract text is available yet for this article.
December 10, 2020: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/33203502/biophysical-studies-of-protein-misfolding-and-aggregation-in-in-vivo-models-of-alzheimer-s-and-parkinson-s-diseases-erratum
#32
JOURNAL ARTICLE
Tessa Sinnige, Karen Stroobants, Christopher M Dobson, Michele Vendruscolo
No abstract text is available yet for this article.
November 18, 2020: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/33148356/single-molecule-studies-of-amyloid-proteins-from-biophysical-properties-to-diagnostic-perspectives
#33
JOURNAL ARTICLE
Jinming Wu, Chan Cao, Rolf Antonie Loch, Ann Tiiman, Jinghui Luo
In neurodegenerative diseases, a wide range of amyloid proteins or peptides such as amyloid-beta and α-synuclein fail to keep native functional conformations, followed by misfolding and self-assembling into a diverse array of aggregates. The aggregates further exert toxicity leading to the dysfunction, degeneration and loss of cells in the affected organs. Due to the disordered structure of the amyloid proteins, endogenous molecules, such as lipids, are prone to interact with amyloid proteins at a low concentration and influence amyloid cytotoxicity...
November 5, 2020: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/33143792/energy-mapping-of-the-genetic-code-and-genomic-domains-implications-for-code-evolution-and-molecular-darwinism
#34
JOURNAL ARTICLE
Horst H Klump, Jens Völker, Kenneth J Breslauer
When the iconic DNA genetic code is expressed in terms of energy differentials, one observes that information embedded in chemical sequences, including some biological outcomes, correlate with distinctive free energy profiles. Specifically, we find correlations between codon usage and codon free energy, suggestive of a thermodynamic selection for codon usage. We also find correlations between what are considered ancient amino acids and high codon free energy values. Such correlations may be reflective of the sequence-based genetic code fundamentally mapping as an energy code...
November 4, 2020: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/32772965/exploring-the-dynamics-of-flagellar-dynein-within-the-axoneme-with-fluctuating-finite-element-analysis
#35
JOURNAL ARTICLE
Robin A Richardson, Benjamin S Hanson, Daniel J Read, Oliver G Harlen, Sarah A Harris
Flagellar dyneins are the molecular motors responsible for producing the propagating bending motions of cilia and flagella. They are located within a densely packed and highly organised super-macromolecular cytoskeletal structure known as the axoneme. Using the mesoscale simulation technique Fluctuating Finite Element Analysis (FFEA), which represents proteins as viscoelastic continuum objects subject to explicit thermal noise, we have quantified the constraints on the range of molecular conformations that can be explored by dynein-c within the crowded architecture of the axoneme...
August 10, 2020: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/32715992/engineering-polymerases-for-applications-in-synthetic-biology
#36
JOURNAL ARTICLE
Ali Nikoomanzar, Nicholas Chim, Eric J Yik, John C Chaput
DNA polymerases play a central role in biology by transferring genetic information from one generation to the next during cell division. Harnessing the power of these enzymes in the laboratory has fueled an increase in biomedical applications that involve the synthesis, amplification, and sequencing of DNA. However, the high substrate specificity exhibited by most naturally occurring DNA polymerases often precludes their use in practical applications that require modified substrates. Moving beyond natural genetic polymers requires sophisticated enzyme-engineering technologies that can be used to direct the evolution of engineered polymerases that function with tailor-made activities...
July 27, 2020: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/32624048/survival-of-the-cheapest-how-proteome-cost-minimization-drives-evolution
#37
JOURNAL ARTICLE
Kasper P Kepp
Darwin's theory of evolution emphasized that positive selection of functional proficiency provides the fitness that ultimately determines the structure of life, a view that has dominated biochemical thinking of enzymes as perfectly optimized for their specific functions. The 20th-century modern synthesis, structural biology, and the central dogma explained the machinery of evolution, and nearly neutral theory explained how selection competes with random fixation dynamics that produce molecular clocks essential e...
June 23, 2020: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/32624046/confined-molecules-experiment-meets-theory-in-small-spaces
#38
JOURNAL ARTICLE
Yang Yu, Julius Rebek
The behavior of molecules confined to small spaces is fascinating chemistry and lies at the heart of signaling processes in biology. Our approach to confinement is through reversible encapsulation of small molecules in synthetic containers. We show that confinement leads to amplified reactivities in bimolecular reactions, stabilization of otherwise reactive species, and limitation in motions that create new stereochemical arrangements. The isolation of molecules from solvent makes for manageable computations and has stimulated theorist to examine reaction details in the limited space...
June 22, 2020: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/32493529/biophysical-studies-of-protein-misfolding-and-aggregation-in-in-vivo-models-of-alzheimer-s-and-parkinson-s-diseases
#39
JOURNAL ARTICLE
Tessa Sinnige, Karen Stroobants, Christopher M Dobson, Michele Vendruscolo
Neurodegenerative disorders, including Alzheimer's (AD) and Parkinson's diseases (PD), are characterised by the formation of aberrant assemblies of misfolded proteins. The discovery of disease-modifying drugs for these disorders is challenging, in part because we still have a limited understanding of their molecular origins. In this review, we discuss how biophysical approaches can help explain the formation of the aberrant conformational states of proteins whose neurotoxic effects underlie these diseases. We discuss in particular models based on the transgenic expression of amyloid-β (Aβ) and tau in AD, and α-synuclein in PD...
June 4, 2020: Quarterly Reviews of Biophysics
https://read.qxmd.com/read/32115014/anionic-food-color-tartrazine-enhances-antibacterial-efficacy-of-histatin-derived-peptide-dhvar4-by-fine-tuning-its-membrane-activity
#40
JOURNAL ARTICLE
Maria Ricci, Kata Horváti, Tünde Juhász, Imola Szigyártó, György Török, Fanni Sebák, Andrea Bodor, László Homolya, Judit Henczkó, Bernadett Pályi, Tamás Mlinkó, Judith Mihály, Bilal Nizami, Zihuayuan Yang, Fengming Lin, Xiaolin Lu, Loránd Románszki, Attila Bóta, Zoltán Varga, Szilvia Bősze, Ferenc Zsila, Tamás Beke-Somfai
Here it is demonstrated how some anionic food additives commonly used in our diet, such as tartrazine (TZ), bind to DHVAR4, an antimicrobial peptide (AMP) derived from oral host defense peptides, resulting in significantly fostered toxic activity against both Gram-positive and Gram-negative bacteria, but not against mammalian cells. Biophysical studies on the DHVAR4-TZ interaction indicate that initially large, positively charged aggregates are formed, but in the presence of lipid bilayers, they rather associate with the membrane surface...
March 2, 2020: Quarterly Reviews of Biophysics
journal
journal
21896
2
3
Fetch more papers »
Fetching more papers... Fetching...
Remove bar
Read by QxMD icon Read
×

Save your favorite articles in one place with a free QxMD account.

×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"

We want to hear from doctors like you!

Take a second to answer a survey question.