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Progress in Biophysics and Molecular Biology

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https://www.readbyqxmd.com/read/30223001/single-molecule-studies-of-flavivirus-envelope-dynamics-experiment-and-computation
#1
REVIEW
Kamal Kant Sharma, Jan K Marzinek, Sarala Neomi Tantirimudalige, Peter J Bond, Thorsten Wohland
Flaviviruses are simple enveloped viruses exhibiting complex structural and functional heterogeneities. Decades of research have provided crucial basic insights, antiviral medication and moderately successful gene therapy trials. The most infectious particle is, however, not always the most abundant one in a population, questioning the utility of classic ensemble-averaging virology approaches. Indeed, viral replication is often not particularly efficient, prone to errors or containing parallel routes. Here, we review different single-molecule sensitive fluorescence methods that are employed to investigate flaviviruses...
September 14, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30217495/structurally-and-dynamically-driven-allostery-of-the-chymotrypsin-like-proteases-of-sars-dengue-and-zika-viruses
#2
REVIEW
Liangzhong Lim, Garvita Gupta, Amrita Roy, Jian Kang, Shagun Srivastava, Jiahai Shi, Jianxing Song
Coronavirus 3C-like and Flavivirus NS2B-NS3 proteases utilize the chymotrypsin fold to harbor their catalytic machineries but also contain additional domains/co-factors. Over the past decade, we aimed to decipher how the extra domains/co-factors mediate the catalytic machineries of SARS 3C-like, Dengue and Zika NS2B-NS3 proteases by characterizing their folding, structures, dynamics and inhibition with NMR, X-ray crystallography and MD simulations, and the results revealed: 1) the chymotrypsin fold of the SARS 3C-like protease can independently fold, while, by contrast, those of Dengue and Zika proteases lack the intrinsic capacity to fold without co-factors...
September 11, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30201490/guiding-principles-for-mechanistic-modeling-of-bispecific-antibodies
#3
Irina Kareva, Anup Zutshi, Senthil Kabilan
System based pharmacokinetic (PK) models can be used to study and predict the distribution of antibody based drugs into target tissues and assess the pharmacobinding (PB) of the drug to the target and the subsequent pharmacodynamic (PD) changes. In the absence of relevant PD readouts, compounded in cases of novel mechanisms, one can rely on binding between the drug and the target, computed as target occupancy (TO), as a relevant biomarker. This approach assumes that at maximum TO across the dosing interval, the drug-target interaction must demonstrate the intended pharmacology...
September 7, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30197289/mechanical-and-morphological-response-of-confluent-epithelial-cell-layers-to-reinforcement-and-dissolution-of-the-f-actin-cytoskeleton
#4
Bastian Rouven Brückner, Helen Nöding, Mark Skamrahl, Andreas Janshoff
The F-actin cytoskeleton and its connection to the plasma membrane provide structure and shape of epithelial cells. In this study we focus on the impact of the F-actin cytoskeleton on the morphology and mechanical behaviour of confluent epithelial cells. F-actin depolymerisation was fostered by Latrunculin A, while depolymerisation was allayed by Jasplakinolide. The impact of drug treatment on cellular mechanics was measured using atomic force microscopy based active microrheology and force-indentation curves, while morphology was monitored by AFM imaging, electric cell-substrate impedance sensing (ECIS) experiments and fluorescence microscopy...
September 6, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30174171/a-model-for-positive-feedback-control-of-the-transformation-of-fibroblasts-to-myofibroblasts
#5
REVIEW
Elliot L Elson, Hong Qian, Judy A Fee, Tetsuro Wakatsuki
The phenotypic conversion of normal fibroblasts to myofibroblasts is central to normal wound healing and to pathological fibrosis that can occur in the heart and many other tissues. The transformation occurs in two stages. The first stage is driven mainly by mechanical changes such as increased stiffness of the heart due to hypertension and cellular contractility. The second stage requires both increasing stiffness and biochemical factors such as the growth factor, TGFβ. As more and more cells convert from weakly contractile fibroblasts to strongly contractile myofibroblasts, the stiffness of the ventricular muscle increases...
August 30, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30171868/structure-and-flexibility-of-non-structural-proteins-3-and-5-of-dengue-and-zika-viruses-in-solution
#6
REVIEW
Wuan Geok Saw, Ankita Pan, Malathy Sony Subramanian Manimekalai, Ardina Grüber, Gerhard Grüber
Dengue- (DENV) and Zika viruses (ZIKV) rely on their non-structural protein 5 (NS5) including a methyl-transferase (MTase) and a RNA-dependent RNA polymerase (RdRp) for capping and synthesis of the viral RNA, and the non-structural protein 3 (NS3) with its protease and helicase domain for polyprotein possessing, unwinding dsRNA proceeding replication, and NTPase/RTPase activities. Accumulation of data for DENV- and ZIKV NS3 and NS5 in solution during recent years provides information about their overall shape, substrate-induced alterations, oligomeric forms and flexibility, with the latter being essential for domain-domain crosstalk...
August 29, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30145156/fitting-two-human-atrial-cell-models-to-experimental-data-using-bayesian-history-matching
#7
Sam Coveney, Richard H Clayton
Cardiac cell models are potentially valuable tools for applications such as quantitative safety pharmacology, but have many parameters. Action potentials in real cardiac cells also vary from beat to beat, and from one cell to another. Calibrating cardiac cell models to experimental observations is difficult, because the parameter space is large and high-dimensional. In this study we have demonstrated the use of history matching to calibrate the maximum conductance of ion channels and exchangers in two detailed models of the human atrial action potential against measurements of action potential biomarkers...
August 24, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30145015/tropomyosin-dynamics-during-cardiac-muscle-contraction-as-governed-by-a-multi-well-energy-landscape
#8
Yasser Aboelkassem, Natalia Trayanova
The dynamic oscillations of tropomyosin molecules in the azimuthal direction over the surface of the actin filament during thin filament activation are studied here from an energy landscape perspective. A mathematical model based on principles from nonlinear dynamics and chaos theory is derived to describe these dynamical motions. In particular, an energy potential with three wells is proposed to govern the tropomyosin oscillations between the observed regulatory positions observed during muscle contraction, namely the blocked "B", closed "C" and open "M" states...
August 22, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30142371/structural-evolution-of-glycyl-trna-synthetases-alpha-subunit-and-its-implication-in-the-initial-organization-of-the-decoding-system
#9
Savio Torres de Farias, Daniel Antonino, Thais Gaudêncio Rêgo, Marco V José
The origin and evolution of the genetic code is a fundamental challenge in modern biology. At the center of this problem is the correct interaction between amino acids and tRNAs. Aminoacyl-tRNA synthetase is the enzyme responsible for the correct binding between amino acids and tRNAs. Among the 20 canonical amino acid, glycine was the most abundant in prebiotic condition and it must have been one of the first to be incorporated into the genetic code. In this work, we derive the ancestral sequence of Glycyl-tRNA synthetase (GlyRS) and predict its 3D-structure...
August 22, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30125585/peptide-based-antimicrobials-design-strategies-and-therapeutic-potential
#10
REVIEW
Prakash Kishore Hazam, Ruchika Goyal, Vibin Ramakrishnan
Therapeutic activity of antibiotics is noteworthy, as they are used in the treatment of microbial infections. Regardless of their utility, there has been a steep decrease in the number of drug candidates due to antibiotic resistance, an inevitable consequence of noncompliance with the full therapeutic regimen. A variety of resistant species like MDR (Multi-Drug Resistant), XDR (Extensively Drug-Resistant) and PDR (Pan Drug-Resistant) species have evolved, but discovery pipeline has already shown signs of getting dried up...
August 18, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30096335/dynamics-of-a-magnetically-rotated-micro-swimmer-inspired-by-paramecium-metachronal-wave
#11
Ali Nematollahisarvestani, Amir Shamloo
In the past few years, a significant body of research has been devoted to designing magnetic micron scale robotic systems for minimally invasive medicine. The motion of different microorganisms is the nature's solution for efficient propulsion of these swimmers. So far, there has been a considerable effort in designing micro swimmers based on the propulsion of bacteria while the motion of numerous other microorganisms has not been a source of inspiration for designing micro swimmers yet. Inspired by propulsion of Paramecium which is a ciliate microorganism, a novel micro swimmer is proposed in this article which is capable of cargo transport...
August 7, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30093083/influence-of-cross-linkers-on-ezrin-bound-minimal-actin-cortices
#12
Markus Schön, Ingo Mey, Claudia Steinem
The actin cortex is a thin network coupled to the plasma membrane of cells, responsible for e.g., cell shape, motility, growth and division. Several model systems for minimal actin cortices (MACs) have been discussed in literature trying to mimic the complex interplay of membrane and actin. We recapitulate on different types of MACs using either three dimensional droplet interfaces or lipid bilayers to which F-actin networks are attached to or planar lipid bilayers with bound actin networks. Binding of the network to the membrane interface significantly influences its properties as well as its dynamics...
August 7, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30078671/age-associated-changes-in-electrical-function-of-the-zebrafish-heart
#13
REVIEW
Matthew R Stoyek, Eva A Rog-Zielinska, T Alexander Quinn
Age-associated changes in cardiac structure and function have been observed from the molecular to whole organ level in humans and mammalian models. Understanding the mechanisms involved is important for explaining the development of cardiac disease with age and developing novel strategies for its treatment and prevention. The zebrafish represents a powerful model for cardiovascular research, as various cardiac pathologies have been recapitulated, it is easily genetically modified, and it is a relatively low cost and high-throughput option...
August 2, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30076851/the-singularity-of-nature
#14
John S Torday
The feasibility of formulating the Singularity of Nature was enunciated by Einstein's mathematical formula, demonstrating the equivalency of energy and mass (E = mc2 ). Despite that statement of principle, it has proven impossible to achieve this goal scientifically by directly merging biology and physics into one continuum. More recently, it has been realized that biology can be traced to its origins by reducing evolutionary biology to cell-cell signaling, the unicellular state being seen as a continuum from genotype to phenotype...
August 1, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30055187/adsorption-of-methylene-blue-on-agroindustrial-wastes-experimental-investigation-and-phenomenological-modelling
#15
L Meili, P V S Lins, M T Costa, R L Almeida, A K S Abud, J I Soletti, G L Dotto, E H Tanabe, L Sellaoui, S H V Carvalho, A Erto
In this work, agro-wastes coming from soursop (peel, seeds and pulp fiber) and sugarcane (bagasse) are used as low-cost biosorbents to remove methylene blue (MB) from aqueous media. Batch experiments are performed under different experimental conditions investigating the effects of biosorbent amount, dye concentration and stirring rate. The best results were found using soursop wastes for a MB concentration of 100 mg L-1 , using 0.75 g of residue and a stirring rate of 110 rpm, removing a percentage above 90%...
July 25, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30036562/mediator-complex-subunit-med12-regulates-cardiac-jelly-development-and-av-valve-formation-in-zebrafish
#16
Julia Segert, Isabelle Schneider, Ina M Berger, Wolfgang Rottbauer, Steffen Just
The molecular mechanism essential for the formation of heart valves involves complex interactions of signaling molecules and transcription factors. The Mediator Complex (MC) functions as multi-subunit machinery to orchestrate gene transcription, especially for tissue-specific fine-tuning of transcriptional processes during development, also in the heart. Here, we analyzed the role of the MC subunit Med12 during atrioventricular canal (AVC) development and endocardial cushion formation, using the Med12-deficient zebrafish mutant trapped (tpd)...
July 20, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30032905/a-beginner-s-guide-to-understanding-and-implementing-the-genetic-modification-of-zebrafish
#17
REVIEW
Sara A Rafferty, T Alexander Quinn
Zebrafish are a relevant and useful vertebrate model species to study normal- and patho-physiology, including that of the heart, due to conservation of protein-coding genes, organ system organisation and function, and efficient breeding and housing. Their amenability to genetic modification, particularly compared to other vertebrate species, is another great advantage, and is the focus of this review. A vast number of genetically engineered zebrafish lines and methods for their creation exist, but their incorporation into research programs is hindered by the overwhelming amount of technical details...
July 19, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30031881/advances-in-mechanism-studies-on-ultrasonic-gene-delivery-at-cellular-level
#18
REVIEW
Jinsui Yu, Zhiyi Chen, Fei Yan
Ultrasound provides a means for intracellular gene delivery, contributing to a noninvasive and spatiotemporally controllable strategy suitable for clinical applications. Many studies have been done to provide mechanisms of ultrasound-mediated gene delivery at the cellular level. This review summarizes the studies on the important aspects of the mechanisms, providing an overview of recent progress in cellular experiment of ultrasound-mediated gene delivery.
July 19, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30031022/pk-pd-based-adaptive-tailoring-of-oseltamivir-doses-to-treat-within-host-influenza-viral-infections
#19
Ghazal Montaseri, Alessandro Boianelli, Esteban A Hernandez-Vargas, Michael Meyer-Hermann
Influenza A virus (IAV) is a latent global threat to human health. In view of the risk of pandemics, prophylactic and curative treatments are essential. Oseltamivir is a neuraminidase inhibitor efficiently supporting recovery from influenza infections. Current common clinical practice is a constant drug dose (75 or 150 mg) administered at regular time intervals twice a day. We aim to use quantitative systems pharmacology to propose an efficient adaptive drug scheduling. We combined the mathematical model for IAV infections validated by murine data, which captures the viral dynamics and the dynamics of the immune host response, with a pharmacokinetic (PK)/pharmacodynamic (PD) model of oseltamivir...
July 19, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30031023/efflux-pumps-and-antimicrobial-resistance-paradoxical-components-in-systems-genomics
#20
REVIEW
Ritika Kabra, Nutan Chauhan, Anurag Kumar, Prajakta Ingale, Shailza Singh
Efflux pumps play a major role in the increasing antimicrobial resistance rendering a large number of drugs of no use. Large numbers of pathogens are becoming multidrug resistant due to inadequate dosage and use of the existing antimicrobials. This leads to the need for identifying new efflux pump inhibitors. Design of novel targeted therapies using inherent complexity involved in the biological network modeling has gained increasing importance in recent times. The predictive approaches should be used to determine antimicrobial activities with high pathogen specificity and microbicidal potency...
July 18, 2018: Progress in Biophysics and Molecular Biology
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