Biophysics

Biophysical characterization and molecular phylogeny of human KIN protein Abstract The DNA/RNA-binding KIN protein was discovered in 1989, and since then, it has been found to participate in several processes, e.g., as a transcription factor in bacteria, yeasts, and plants, in immunoglobulin isotype switching, and in the repair and resolution of double-strand breaks caused by ionizing radiation. However, the complete three-dimensional structure and biophysical properties of KIN remain important information for clarifying its function and to help elucidate mechanisms associated with it not yet completely understood. The present study provides data on phylogenetic analyses of the different domains, as well as a biophysical characterization of the human KIN protein (HSAKIN) using bioinformatics techniques, circular dichroism spectroscopy, and differential scanning calorimetry to estimate the composition of secondary structure elements; further studies were performed to determine the biophysical parameters ΔHm and Tm. The phylogenetic analysis indicated that the zinc-finger and winged helix domains are highly conserved in KIN, with mean identity of 90.37% and 65.36%, respectively. The KOW motif was conserved only among the higher eukaryotes, indicating that this motif emerged later on the evolutionary timescale. HSAKIN has more than 50% of its secondary structure composed by random coil and β-turns. The highest values of ΔHm and Tmwere found at pH 7.4 suggesting a stable structure at physiological conditions. The characteristics found for HSAKIN are primarily due to its relatively low composition of α-helices and β-strands, making up less than half of the protein structure.

57 Fe enrichment in mice for β-thalassaemia studies via Mössbauer spectroscopy of blood samples Abstract In this work, wild-type and heterozygous β-thalassaemic mice were enriched with 57Fe via gastrointestinal absorption to characterize in greater detail the iron complexes then identifiable via Mössbauer spectroscopy. The 57Fe enrichment method was validated and Mössbauer spectra were obtained at 80 K from blood samples from wild-type and β-thalassaemic mice at 1, 3, 6, and 9 months of age. As expected, the haemoglobin levels of the thalassaemic mice were lower than from normal mice, indicating anaemia. Furthermore, significant amounts of ferritin-like iron were observed in the thalassaemic mice samples, which decreased with mouse age, reflecting the pattern of reticulocyte count reduction reported in the literature.

Growth of a gas bubble in a perfused tissue in an unsteady pressure field with source or sink Abstract In the context of decompression sickness, this paper presents analytical formulae and explanations for growth of a gas bubble in blood and other tissues in an unsteady diffusion field with a source or a sink. The formulae are valid for variable (through decompression) and constant (concerning diving stops/at sea level) ambient pressure. Under a linear decompression regime for ambient pressure, the gas bubble growth is proportional to ascent rate, tissue diffusivity and initial tissue tension and inversely proportional to surface tension, initial ambient pressure and the strength of the source/sink parameter \(k\) which gives the conditions for bubble growth. We find that the growth process is noticeably affected by changing k-values within a specified range, with no significant effect on the value of the bubble radius when k is outside this range. We discuss the effect of the presence of multiple bubbles, and of repetitive diving. Of the three available models for bubble growth, the predicted time to completion is longest in the model by Srinivasan et al. (J Appl Physiol 86:732–741, 1999), where the bubble grows in a steady diffusion field, but shortest in the model we describe for k-values closest to the boundaries of the interval \([0. 9 5 8 7,\;\;1.0]\) . This is because our model considers the effect of the presence of a source, increasing the bubble growth rate and not taken into account in our previous (2010) model predicting an intermediate timeframe for bubble growth. We believe our new model provides a more accurate and widely applicable description of bubble growth in decompression sickness than previous versions.

Viscoelasticity variation in a biofilm-mediated Bacillus subtilis suspension induced by adding polyethylene glycol Abstract Recent experiments show that synthetic polymers can influence the degree of microbial aggregation and the rheological properties of bacterial suspensions, the study of which can help us control biofilm formation. In this article, we add polyethylene glycol (PEG) with various molecular weights and concentrations into two types Bacillus subtilis cell cultures, Luria Broth (LB) and Minimal Salts glutamate glycerol (MSgg), respectively. We first observe cell clusters in cell suspensions with various concentrations of PEG, and measure cluster size in both static and dynamic fluid environments. We find that cells gather together into big clusters and most of the cells are arranged longitudinally; and the large cell clusters are divided into smaller aggregates under fluid shear. We then use a rheometer to measure the viscoelastic properties of various cell cultures, to represent the degree of aggregation of the bacterial suspensions. We find the storage modulus, the loss modulus and the viscosity of bacterial suspensions not only depend on the cell aggregation but also depend on the directionality of cellular motion.

Are cell membrane nanotubes the ancestors of the nervous system? Abstract Cell membrane nanotubes, variously referred to as tunneling nanotubes and cytonemes, are currently the focus of much interest. They are of ancient origin, as indicated by their opportunistic use for cell invasion by pathogens, including bacteria and virus, and by their employment in bacterial networking. They play a significant role in cancer invasion and in the explanation of glioblastoma resistance to treatment. Their structure and properties have been investigated with optical tweezers. They have been detected in vivo. Their role in the immune system was early verified. Very recently, it was shown that they share many properties with nerve synapses, including the roles of glutamate and Ca ions. Similar features have also been observed in primitive plants. These results support the conjecture that, besides their roles in immunology, developmental biology and cancer, cell membrane nanotubes are the ancestors of the nervous system.

A model for the chemomechanical coupling of the mammalian cytoplasmic dynein molecular motor Abstract Available single-molecule data have shown that some mammalian cytoplasmic dynein dimers move on microtubules with a constant step size of about 8.2 nm. Here, a model is presented for the chemomechanical coupling of these mammalian cytoplasmic dynein dimers. In contrast to the previous models, a peculiar feature of the current model is that the rate constants of ATPase activity are independent of the external force. Based on this model, analytical studies of the motor dynamics are presented. With only four adjustable parameters, the theoretical results reproduce quantitatively diverse available single-molecule data on the force dependence of stepping ratio, velocity, mean dwell time, and dwell-time distribution between two mechanical steps. Predicted results are also provided for the force dependence of the number of ATP molecules consumed per mechanical step, indicating that under no or low force the motors exhibit a tight chemomechanical coupling, and as the force increases the number of ATPs consumed per step increases greatly.

Network analysis of dynamically important residues in protein structures mediating ligand-binding conformational changes Abstract According to the generalized conformational selection model, ligand binding involves the co-existence of at least two conformers with different ligand-affinities in a dynamical equilibrium. Conformational transitions between them should be guaranteed by intramolecular vibrational dynamics associated to each conformation. These motions are, therefore, related to the biological function of a protein. Positions whose mutations are found to alter these vibrations the most can be defined as key positions, that is, dynamically important residues that mediate the ligand-binding conformational change. In a previous study, we have shown that these positions are evolutionarily conserved. They correspond to buried aliphatic residues mostly localized in regular structured regions of the protein like β-sheets and α-helices. In the present paper, we perform a network analysis of these key positions for a large dataset of paired protein structures in the ligand-free and ligand-bound form. We observe that networks of interactions between these key positions present larger and more integrated networks with faster transmission of the information. Besides, networks of residues result that are robust to conformational changes. Our results reveal that the conformational diversity of proteins seems to be guaranteed by a network of strongly interconnected key positions rather than individual residues.

JOINT 12 th EBSA congress and 10 th ICBP – IUPAP congress, July 20-24, 2019, Madrid, Spain – Abstracts

Regional Biophysics Conference: RBC2018

Biophysical modeling of wave propagation phenomena: experimental determination of pulse wave velocity in viscous fluid-filled elastic tubes in a gravitation field Abstract Biophysical understanding of arterial hemodynamics plays an important role in proper medical diagnosis and investigation of cardiovascular disease pathogens. One of the major cardiovascular parameters is pulse wave velocity (PWV), which depends on the mechanical properties of the arterial wall. The PWV contains information on the condition of the cardiovascular system as well as its physiological age. In humans and most animals, blood flow through the blood vessels is affected by several internal and external forces. The most influencing external force on blood flow is gravity. In the upright position of the body, blood moves from heart to head, opposite to gravity, and from the heart to the legs, in direction of the gravitational force. To investigate how gravity affects PWV, we have developed a biophysical model of cardiovascular system that simulates blood flow in the upright position of the body. The paper presents the results of measurement of PWV in an elastic tube filled with fluids of different viscosities in the gravitational field.