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Progress in Biophysics and Molecular Biology

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https://www.readbyqxmd.com/read/30365971/an-extremely-low-frequency-weak-magnetic-field-can-induce-alterations-in-a-biological-system-a-case-study-in-chick-embryo-development
#1
Ahmed El-Hussein, M A Kasem, Abd El Hakim Saad, Michael R Hamblin, M A Harith
The aim of the current study was to investigate the effects of a weak magnetic field at extremely low frequency on a biological system. Our case study was on chick embryo development. Freshly fertilized chicken eggs were subjected to magnetic field (1.0 μT peak-to-peak amplitude) for 48 h immediately after laying. Following exposure, eggs were incubated for more 9 days without any magnetic stimuli. The exposed embryos show developmental anomalies compared with sham-exposed controls. Histopathological features were identified in slides prepared from chick embryos using optical microscopy...
October 23, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30359669/higher-peptide-nonplanarity-%C3%AF-close-to-protein-carboxy-terminal-and-its-positive-correlation-with-%C3%AF-dihedral-angle-is-evolved-conferring-protein-thermostability
#2
Smarajit Maiti, Anindya Sundar Panja, Bidyut Bandopadhyay
BACKGROUND: Thermostability conferred by ensembles of several weak-interactions results in compactness-rigidity in proteins that impairs their flexibility/function. Understanding of protein's structural modification under stress is important. METHOD: In this study, randomly selected 54 nonhomologous and variedly thermostable (0-20 °C/21-40 °C/41-60 °C/61-80 °C/81-100 °C) proteins were investigated to elucidate their thermostability utilizing multiple bioinformatics-tools...
October 23, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30336184/biological-evolution-as-defense-of-self
#3
William B Miller, John S Torday, František Baluška
Although the origin of self-referential consciousness is unknown, it can be argued that the instantiation of self-reference was the commencement of the living state as phenomenal experientiality. As self-referential cognition is demonstrated by all living organisms, life can be equated with the sustenance of cellular homeostasis in the continuous defense of 'self'. It is proposed that the epicenter of 'self' is perpetually embodied within the basic cellular form in which it was instantiated. Cognition-Based Evolution argues that all of biological and evolutionary development represents the perpetual autopoietic defense of self-referential basal cellular states of homeostatic preference...
October 16, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30312622/systems-variation-individuality-and-plant-hormones
#4
REVIEW
Masaaki Watahiki, Anthony Trewavas
Inter-individual variation in plants and particularly in hormone content, figures strongly in evolution and behaviour. Homo sapiens and Arabidopsis exhibit similar and substantial phenotypic and molecular variation. Whereas there is a very substantial degree of hormone variation in mankind, reports of inter-individual variation in plant hormone content are virtually absent but are likely to be as large if not larger than that in mankind. Reasons for this absence are discussed. Using an example of inter-individual variation in ethylene content in ripening, the article shows how biological time is compressed by hormones...
October 9, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30291845/conformational-states-of-zika-virus-non-structural-protein-3-determined-by-molecular-dynamics-simulations-with-small-angle-x-ray-scattering-data
#5
Guanhua Zhu, Ankita Pan, Gerhard Grüber, Lanyuan Lu
Zika virus (ZIKV) has become a great public health emergency. Its non-structural protein 3 (NS3) is a key enzyme in viral replication and has been considered as a potential therapeutic target. A conformational characterization of ZIKV NS3 is critical for a comprehensive understanding of its molecular interactions and functions. However, the high conformational flexibility of solution NS3 obstacles the structural characterization of NS3 solely from the experimental observable that averages over its heterogeneous conformations...
October 3, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30273615/coarse-grained-dynamics-of-supramolecules-conformational-changes-in-outer-shells-of-dengue-viruses
#6
Patrice Koehl, Marc Delarue
While structural data on viruses are more and more common, information on their dynamics is much harder to obtain as those viruses form very large molecular complexes. In this paper, we propose a new method for computing the coarse-grained normal modes of such supra-molecules, NormalGo. A new formalism is developed to represent the Hessian of a quadratic potential using tensor products. This formalism is applied to the Tirion elastic potential, as well as to a Gō like potential. When combined with a fast method for computing a select set of eigenpairs of the Hessian, this new formalism enables the computation of thousands of normal modes of a full viral shell with more than one hundred thousand atoms in less than 2 h on a standard desktop computer...
September 28, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30267722/differential-diffusivity-of-the-turing-morphogens
#7
Yoram Schiffmann
The Turing morphogens cAMP and ATP are considered as electrolytes. Each is made of a slow anion and fast cation. The unequal diffusion of the of the cation and the anion creates an electric field which accelerates the anion and decelerates the cation. This effect is more pronounced for ATP than cAMP since ATP has higher charge and greater concentration than cAMP.
September 27, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30244089/numerical-analysis-of-steele-et-al-2018-cause-of-cambrian-explosion-terrestrial-or-cosmic
#8
LETTER
Ronald G Duggleby
No abstract text is available yet for this article.
September 20, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30243548/the-electrocardiogram-of-vertebrates-evolutionary-changes-from-ectothermy-to-endothermy
#9
REVIEW
Bastiaan J D Boukens, Ditte L Kristensen, Renato Filogonio, Laura B T Carreira, Marina R Sartori, Augusto S Abe, Shannon Currie, William Joyce, Justin Conner, Tobias Opthof, Dane A Crossley, Tobias Wang, Bjarke Jensen
The electrocardiogram (ECG) reveals that heart chamber activation and repolarization are much faster in mammals and birds compared to ectothermic vertebrates of similar size. Temperature, however, affects electrophysiology of the heart and most data from ectotherms are determined at body temperatures lower than those of mammals and birds. The present manuscript is a review of the effects of temperature on intervals in the ECG of ectothermic and endothermic vertebrates rather than a hypothesis-testing original research article...
September 19, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30241906/the-role-of-the-gap-junction-perinexus-in-cardiac-conduction-potential-as-a-novel-anti-arrhythmic-drug-target
#10
REVIEW
Daniel T Hoagland, Webster Santos, Steven Poelzing, Robert G Gourdie
Cardiovascular disease remains the single largest cause of natural death in the United States, with a significant cause of mortality associated with cardiac arrhythmias. Presently, options for treating and preventing myocardial electrical dysfunction, including sudden cardiac death, are limited. Recent studies have indicated that conduction of electrical activation in the heart may have an ephaptic component, wherein intercellular coupling occurs via electrochemical signaling across narrow extracellular clefts between cardiomyocytes...
September 18, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/30223001/single-molecule-studies-of-flavivirus-envelope-dynamics-experiment-and-computation
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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