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Biophysical Reviews

Satoshi Takahashi, Aya Yoshida, Hiroyuki Oikawa
We propose a hypothesis that explains two apparently contradicting observations for the heterogeneity of the unfolded proteins. First, the line confocal method of the single-molecule Förster resonance energy transfer (sm-FRET) spectroscopy revealed that the unfolded proteins possess broad peaks in the FRET efficiency plot, implying the significant heterogeneity that lasts longer than milliseconds. Second, the fluorescence correlation method demonstrated that the unfolded proteins fluctuate in the time scale shorter than 100 ns...
February 14, 2018: Biophysical Reviews
Muhamad Sahlan, Tamotsu Zako, Masafumi Yohda
Prefoldin is a hexameric molecular chaperone found in the cytosol of archaea and eukaryotes. Its hexameric complex is built from two related classes of subunits and has the appearance of a jellyfish: its body consists of a double beta-barrel assembly with six long tentacle-like coiled coils protruding from it. Using the tentacles, prefoldin captures an unfolded protein substrate and transfers it to a group II chaperonin. The prefoldin-group II chaperonin system is thought to be important for the folding of newly synthesized proteins and for their maintenance, or proteostasis, in the cytosol...
February 9, 2018: Biophysical Reviews
Debasis Saha, Arnab Mukherjee
The remarkable progress in the field of ionic liquids (ILs) in the last two decades has involved investigations on different aspects of ILs in various conditions. The nontoxic and biocompatible nature of ILs makes them a suitable substance for the storage and application of biomolecules. In this regard, the aqueous IL solutions have attracted a large number of studies to comprehend the role of water in modulating various properties of biomolecules. Here, we review some of the recent studies on aqueous ILs that concern the role of water in altering the behavior of ILs in general and in case of biomolecules solvated in ILs...
February 8, 2018: Biophysical Reviews
Fumio Arisaka
This short biographical note was written as part of the lead-in material for a festschrift kindly organized for me on the occasion of my 70th birthday. The collection of articles assembled in this issue range within the spectrum of the topics covered in the special issue 'Multiscale structural biology-biophysical principles and practice ranging from biomolecules to bionanomachines.' Here I describe some of the high points of my 40 years of research science conducted in the USA, Switzerland and Japan. I also use this opportunity to express my sincerest thanks to my former colleagues and the very many contributors who so kindly contributed to this special issue...
February 6, 2018: Biophysical Reviews
Peter Schuck
No abstract text is available yet for this article.
February 6, 2018: Biophysical Reviews
C G Dos Remedios, S P Lal, A Li, J McNamara, A Keogh, P S Macdonald, R Cooke, E Ehler, R Knöll, S B Marston, J Stelzer, H Granzier, C Bezzina, S van Dijk, F De Man, G J M Stienen, J Odeberg, F Pontén, W A Linke, J van der Velden
In the original version of this article, the name of one of the authors is not correct. The correct name should be W. A. Linke, which is shown correctly in the authorgroup section above.
February 1, 2018: Biophysical Reviews
Christina Papini, Catherine A Royer
Biological function results from properly timed bio-molecular interactions that transduce external or internal signals, resulting in any number of cellular fates, including triggering of cell-state transitions (division, differentiation, transformation, apoptosis), metabolic homeostasis and adjustment to changing physical or nutritional environments, amongst many more. These bio-molecular interactions can be modulated by chemical modifications of proteins, nucleic acids, lipids and other small molecules. They can result in bio-molecular transport from one cellular compartment to the other and often trigger specific enzyme activities involved in bio-molecular synthesis, modification or degradation...
January 30, 2018: Biophysical Reviews
Donald J Winzor, David J Scott
This review summarizes endeavors undertaken in the middle of last century to employ the Lamm equation for quantitative analysis of boundary spreading in sedimentation velocity experiments on globular proteins, thereby illustrating the ingenuity required to achieve that goal in an era when an approximate analytical solution of that nonlinear differential equation of second order provided the only means for its application. Application of procedures based on that approximate solution to simulated sedimentation velocity distributions has revealed a slight disparity (about 3%) between returned and input values of the diffusion coefficient-a discrepancy comparable with that of estimates obtained by current simulative analyses based on numerical solution of the Lamm equation...
January 27, 2018: Biophysical Reviews
Walter Herzog
Titin is a filamentous protein spanning the half-sarcomere, with spring-like properties in the I-band region. Various structural, signaling, and mechanical functions have been associated with titin, but not all of these are fully elucidated and accepted in the scientific community. Here, I discuss the primary mechanical functions of titin, including its accepted role in passive force production, stabilization of half-sarcomeres and sarcomeres, and its controversial contribution to residual force enhancement, passive force enhancement, energetics, and work production in shortening muscle...
January 20, 2018: Biophysical Reviews
Cristobal G Dos Remedios
In 2017, a Special Issue of Biophysical Reviews was devoted to "Titin and Its Binding Partners. The issue contained a review: "An historical perspective of the discovery of titin filaments" by dos Remedios and Gilmour that was intended to be a history of the discovery of the giant protein titin, previously named connectin. The review took readers back to the earliest discovery of the so-called third filament component of skeletal and cardiac muscle sarcomeres and ended in 1969. Recently, my colleague Shin'ichi Ishiwata gently reminded me of two papers published in 1990 and 1993 that were unwittingly omitted from the original historical perspective...
January 13, 2018: Biophysical Reviews
Tamkin Ahmadzada, Glen Reid, David R McKenzie
Gene silencing via RNA interference (RNAi) is rapidly evolving as a personalized approach to cancer treatment. The effector molecules-small interfering RNAs (siRNAs) and microRNAs (miRNAs)-can be used to silence or "switch off" specific cancer genes. Currently, the main barrier to implementing siRNA- and miRNA-based therapies in clinical practice is the lack of an effective delivery system that can protect the RNA molecules from nuclease degradation, deliver to them to tumor tissue, and release them into the cytoplasm of the target cancer cells, all without inducing adverse effects...
January 11, 2018: Biophysical Reviews
Wojciech Chrzanowski, Anna V Ceguerra
No abstract text is available yet for this article.
January 10, 2018: Biophysical Reviews
Ksenia S Egorova, Valentine P Ananikov
Comparison of chemical catalysis by metal complexes, enzymatic catalysis and whole-cell biocatalysis shows well-addressed advantages of the latter approach. However, a critical limitation in the practical applications originates from the high sensitivity of microorganisms to the toxic effects of organic solvents. In the present review, we consider toxic solvent properties of ionic liquid/water systems towards the development of efficient applications in practical organic transformations.
January 8, 2018: Biophysical Reviews
Munehito Arai
Extensive experimental and theoretical studies have advanced our understanding of the mechanisms of folding and binding of globular proteins, and coupled folding and binding of intrinsically disordered proteins (IDPs). The forces responsible for conformational changes and binding are common in both proteins; however, these mechanisms have been separately discussed. Here, we attempt to integrate the mechanisms of coupled folding and binding of IDPs, folding of small and multi-subdomain proteins, folding of multimeric proteins, and ligand binding of globular proteins in terms of conformational selection and induced-fit mechanisms as well as the nucleation-condensation mechanism that is intermediate between them...
January 6, 2018: Biophysical Reviews
G Bhattacharya, S Mitra, P Mandal, S Dutta, R P Giri, S K Ghosh
Understanding the interaction of ionic liquids with cellular membrane becomes utterly important to comprehend the activities of these liquids in living organisms. Lipid monolayer formed at the air-water interface is employed as a model system to follow this interaction by investigating important thermodynamic parameters. The penetration kinetics of the imidazolium-based ionic liquid 1-decyl-3-methylimidazolium tetrafluoroborate ([DMIM][BF4]) into the zwitterionic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid layer is found to follow the Boltzmann-like equation that reveals the characteristic time constant which is observed to be the function of initial surface pressure...
January 5, 2018: Biophysical Reviews
Da Wang, Hans-Joachim Galla, Patrick Drücker
Room-temperature ionic liquids (RTILs) have attracted considerable attention in recent years due to their versatile properties such as negligible volatility, inflammability, high extractive selectivity and thermal stability. In general, RTILs are organic salts with a melting point below ~100 °C determined by the asymmetry of at least one of their ions. Due to their amphiphilic character, strong interactions with biological materials can be expected. However, rising attention has appeared towards their similarity and interaction with biomolecules...
January 4, 2018: Biophysical Reviews
Yutaka Kuroda
At concentrations above solubility, a protein aggregates, most often into amorphous aggregates, and loses its function. However, unlike amyloidogenic aggregates, which are β-sheeted fibrillar aggregates often related to neurodegenerative diseases, amorphous aggregates, where proteins aggregate/oligomerize without forming specific high-order structures, are rarely the focus of biophysical studies. Hence, protein solubility with respect to amorphous aggregation remains to be fully characterized from a biophysical viewpoint...
January 4, 2018: Biophysical Reviews
Ahmed S A Dowah, Martha R J Clokie
As the importance of bacteriophages as novel antimicrobials and potential diagnostics comes increasingly into focus, there is a heightened interest in understanding the mechanisms of how they interact with their bacterial hosts. The first step of a bacteriophage (phage) infection is the recognition of specific moieties on the bacterial cell surface as determined by their phage receptor binding proteins (RBPs). Knowledge of RBPs and how they interact with bacteria has been driven by studies of model phages and of industrially important phages, such as those that impact the dairy industry...
January 3, 2018: Biophysical Reviews
Emanuelle L P de Faria, Melissa V Gomes, Ana Filipa M Cláudio, Carmen S R Freire, Armando J D Silvestre, Mara G Freire
Due to the wide range of relevant biological activities and high commercial value of cynaropicrin, and aiming at developing cost-effective processes, aqueous solutions of ionic liquids (ILs) were investigated for the extraction and recovery of cynaropicrin from the leaves of Cynara cardunculus L. Both cationic (1-alkyl-3-methylimidazolium chloride) and anionic (cholinium carboxylate) surface-active ILs were investigated, as well as a wide range of conventional surfactants and molecular organic solvents, allowing us to conclude that aqueous solutions of cationic surface-active ILs display a better performance for the extraction of cynaropicrin...
January 2, 2018: Biophysical Reviews
Karuna Anna Sajeevan, Durba Roy
The appearance of several disulfide bond isoforms in multiple cysteine containing venom peptides poses a significant challenge in their synthesis and purification under laboratory conditions. Recent experiments suggest that careful tuning of solvent and temperature conditions can propel the disulfide bond isoform equilibrium in favor of the most potent, native form. Certain aqueous ionic liquids (ILs) have proven significantly useful as solvents for this purpose, while exceptions have also been noted. To elucidate the molecular level origin behind such a preference, we report a detailed explicit solvent replica exchange molecular dynamics study of a conotoxin, AuIB, in pure water and four different aqueous IL solutions (~45-60% v/v)...
January 2, 2018: Biophysical Reviews
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