Rigidity loss of protein macromolecule induced by force—Effective field theory

In the framework of the effective field theory for the order parameter, which characterizes the degree of deviating the protein globule structure from its native state, the phase transition of the protein macromolecule from the elastic state into the plastic one under its mechanical stretching is considered. Elastic properties of a protein are studied as a function of the applied force, temperature, and the mean coordination number of the protein “network.” Proteins 2014; 82:966–974. © 2013 Wiley Periodicals, Inc.     

Sequence and domain arrangements influence mechanical properties of elastin‐like polymeric elastomers

Elastin is the polymeric, extracellular matrix protein that provides properties of extensibility and elastic recoil to large arteries, lung parenchyma, and other tissues. Elastin assembles by crosslinking through lysine residues of its monomeric precursor, tropoelastin. Tropoelastin, as well as polypeptides based on tropoelastin sequences, undergo a process of self‐assembly that aligns lysine residues for crosslinking. As a result, both the full‐length monomer as well as elastin‐like polypeptides (ELPs) can be made into biomaterials whose properties resemble those of native polymeric elastin. Using both full‐length human tropoelastin (hTE) as well as ELPs, we and others have previously reported on the influence of sequence and domain arrangements on self‐assembly properties. Here we investigate the role of domain sequence and organization on the tensile mechanical properties of crosslinked biomaterials fabricated from ELP variants. In general, substitutions in ELPs involving similiar domain types (hydrophobic or crosslinking) had little effect on mechanical properties. However, modifications altering either the structure or the characteristic sequence style of these domains had significant effects on such properties. In addition, using a series of deletion and replacement constructs for full‐length hTE, we provide new insights into the role of conserved domains of tropoelastin in determining mechanical properties. © 2012 Wiley Periodicals, Inc. Biopolymers 99: 392–407, 2013.     

Protein side‐chain modeling with a protein‐dependent optimized rotamer library

Despite years of effort, the problem of predicting the conformations of protein side chains remains a subject of inquiry. This problem has three major issues, namely defining the conformations that a side chain may adopt within a protein, developing a sampling procedure for generating possible side‐chain packings, and defining a scoring function that can rank these possible packings. To solve the former of these issues, most procedures rely on a rotamer library derived from databases of known protein structures. We introduce an alternative method that is free of statistics. We begin with a rotamer library that is based only on stereochemical considerations; this rotamer library is then optimized independently for each protein under study. We show that this optimization step restores the diversity of conformations observed in native proteins. We combine this protein‐dependent rotamer library (PDRL) method with the self‐consistent mean field (SCMF) sampling approach and a physics‐based scoring function into a new side‐chain prediction method, SCMF–PDRL. Using two large test sets of 831 and 378 proteins, respectively, we show that this new method compares favorably with competing methods such as SCAP, OPUS‐Rota, and SCWRL4 for energy‐minimized structures. Proteins 2014; 82:2000–2017. © 2014 Wiley Periodicals, Inc.     

Combining near‐ and far‐field exposure for an organ‐specific and whole‐body RF‐EMF proxy for epidemiological research: A reference case

A framework for the combination of near‐field (NF) and far‐field (FF) radio frequency electromagnetic exposure sources to the average organ and whole‐body specific absorption rates (SARs) is presented. As a reference case, values based on numerically derived SARs for whole‐body and individual organs and tissues are combined with realistic exposure data, which have been collected using personal exposure meters during the Swiss Qualifex study. The framework presented can be applied to any study region where exposure data is collected by appropriate measurement equipment. Based on results derived from the data for the region of Basel, Switzerland, the relative importance of NF and FF sources to the personal exposure is examined for three different study groups. The results show that a 24‐h whole‐body averaged exposure of a typical mobile phone user is dominated by the use of his or her own mobile phone when a Global System for Mobile Communications (GSM) 900 or GSM 1800 phone is used. If only Universal Mobile Telecommunications System (UMTS) phones are used, the user would experience a lower exposure level on average caused by the lower average output power of UMTS phones. Data presented clearly indicate the necessity of collecting band‐selective exposure data in epidemiological studies related to electromagnetic fields. Bioelectromagnetics 34:366–374, 2013. © 2012 Wiley Periodicals, Inc.     

Caveolin‐1 down‐regulation is required for Wnt5a‐Frizzled 2 signalling in Ha‐RasV12‐induced cell transformation

Caveolin‐1 (Cav1) is down‐regulated during MK4 (MDCK cells harbouring inducible Ha‐Ras^V12 gene) transformation by Ha‐Ras^V12. Cav1 overexpression abrogates the Ha‐Ras^V12‐driven transformation of MK4 cells; however, the targeted down‐regulation of Cav1 is not sufficient to mimic this transformation. Cav1‐silenced cells, including MK4/shCav1 cells and MDCK/shCav1 cells, showed an increased cell area and discontinuous junction‐related proteins staining. Cellular and mechanical transformations were completed when MDCK/shCav1 cells were treated with medium conditioned by MK4 cells treated with IPTG (MK4+I‐CM) but not with medium conditioned by MK4 cells. Nanoparticle tracking analysis showed that Ha‐Ras^V12‐inducing MK4 cells increased exosome‐like microvesicles release compared with their normal counterparts. The cellular and mechanical transformation activities of MK4+I‐CM were abolished after heat treatment and exosome depletion and were copied by exosomes derived from MK4+I‐CM (MK4+I‐EXs). Wnt5a, a downstream product of Ha‐Ras^V12, was markedly secreted by MK4+I‐CM and MK4+I‐EXs. Suppression of Wnt5a expression and secretion using the porcupine inhibitor C59 or Wnt5a siRNA inhibited the Ha‐Ras^V12‐ and MK4+I‐CM‐induced transformation of MK4 cells and MDCK/shCav1 cells, respectively. Cav1 down‐regulation, either by Ha‐Ras^V12 or targeted shRNA, increased frizzled‐2 (Fzd2) protein levels without affecting its mRNA levels, suggesting a novel role of Cav1 in negatively regulating Fzd2 expression. Additionally, silencing Cav1 facilitated the internalization of MK4+I‐EXs in MDCK cells. These data suggest that Cav1‐dependent repression of Fzd2 and exosome uptake is potentially relevant to its antitransformation activity, which hinders the activation of Ha‐Ras^V12‐Wnt5a‐Stat3 pathway. Altogether, these results suggest that both decreasing Cav1 and increasing exosomal Wnt5a must be implemented during Ha‐Ras^V12‐driven cell transformation.     

Interactions of macromolecules with salt ions: an electrostatic theory for the Hofmeister effect

Salting-out of proteins was discovered in the nineteenth century and is widely used for protein separation and crystallization. It is generally believed that salting-out occurs because at high concentrations salts and the protein compete for solvation water. Debye and Kirkwood suggested ideas for explaining salting-out (Debeye and MacAulay, Physik Z; 1925;131:22-29; Kirkwood, In: Proteins, amino acids and peptides as ions and dipolar ions. New York: Reinhold; 1943. p 586-622). However, a quantitative theory has not been developed, and such a theory is presented here. It is built on Kirkwood's idea that a salt ion has a repulsive interaction with an image charge inside a low dielectric cavity. Explicit treatment is given for the effect of other salt ions on the interaction between a salt ion and its image charge. When combined with the Debye-Hückel effect of salts on the solvation energy of protein charges (i.e., salting-in), the characteristic curve of protein solubility versus salt concentration is obtained. The theory yields a direct link between the salting-out effect and surface tension and is able to provide rationalizations for the effects of salt on the folding stability of several proteins.     

Neural field theory of synaptic plasticity

Plasticity is crucial to neural development, learning, and memory. In the common in vivo situation where postsynaptic neural activity results from multiple presynaptic inputs, it is shown that a widely used class of correlation-dependent and spike-timing dependent plasticity rules can be written in a form that can be incorporated into neural field theory, which enables their system-level dynamics to be investigated. It is shown that the resulting plasticity dynamics depends strongly on the stimulus spectrum via overall system frequency responses. In the case of perturbations that are approximately linear, explicit formulas are found for the dynamics in terms of stimulus spectra via system transfer functions. The resulting theory is applied to a simple model system to reveal how collective effects, especially resonances, can drastically modify system-level plasticity dynamics from that implied by single-neuron analyses. The simplified model illustrates the potential relevance of these effects in applications to brain stimulation, synaptic homeostasis, and epilepsy.     

Controlling network topology and mechanical properties of co‐assembling peptide hydrogels

Oligopeptides are well‐known to self‐assemble into a wide array of nanostructures including β‐sheet‐rich fibers that when present above a critical concentration become entangled and form self‐supporting hydrogels. The length, quantity, and interactions between fibers influence the mechanical properties of the hydrogel formed and this is typically achieved by varying the peptide concentration, pH, ionic strength, or the addition of a second species or chemical cross‐linking agent. Here, we outline an alternative, facile route to control the mechanical properties of the self‐assembling octa‐peptide, FEFEFKFK (FEKII); simply doping with controlled quantities of its double length peptide, FEFEFKFK‐GG‐FKFKFEFE (FEKII18). The structure and properties of a series of samples were studied here (0–100 M% of FEKII18) using Fourier transform infrared, small angle X‐ray scattering, transmission electron microscopy, and oscillatory rheology. All samples were found to contain elongated, flexible fibers and all mixed samples contained Y‐shaped branch points and parallel fibers which is attributed to the longer peptide self‐assembling within two fibers, thus creating a cross‐link in the network structure. Such behavior was reflected in an increase in the elasticity of the mixed samples with increasing quantity of double peptide. Interestingly the elastic modulus increased up to 30 times the pure FEKII value simply by adding 28 M% of FEKII18. These observations provide an easy, off‐the‐shelf method for an end‐user to control the cross‐linked network structure of the peptide hydrogel, and consequently strength of the hydrogel simply by physically mixing pre‐determined quantities of two similar peptide molecules. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 669–680, 2014.     

Neurobiological effects of pulsed magnetic field on diabetes‐induced neuropathy

In the clinic, although several pharmacological agents or surgical procedures are used to treat diabetes and diabetes‐induced neuropathic pain, their success has been limited. Therefore, development of different alternatives in treatments is very important. The purpose of this study was to determine the efficacy of pulsed magnetic field (PMF) in improving signs and symptoms of diabetic neuropathy. In this study, the effects of PMF treatment were investigated in Streptozotocin (STZ)‐induced acute and chronic diabetic rats by measuring the thermal latencies, mechanical thresholds, whole blood glucose levels and body weights. After STZ administration to rats, blood glucose level elevated and body weight decreased. Although PMF treatment did not affect changes in body weight, the blood glucose levels of PMF‐treated diabetic rats exhibited a decrease during the treatments. Diabetic animals displayed marked decrease in mechanical thresholds and thermal latencies. While treatment of PMF partially restored the mechanical thresholds and thermal latency in acute diabetic rats, PMF caused a corrective effect on only mechanical threshold of chronic diabetic rats. These results suggested that treatment of PMF can potentially ameliorate the painful symptoms of diabetes, such as hyperalgesia and allodynia, by partially preventing the hyperglycemia. Bioelectromagnetics 31:39–47, 2010. © 2009 Wiley‐Liss, Inc.     

Hydrogel‐based three‐dimensional cell culture for organ‐on‐a‐chip applications

Recent studies have reported that three‐dimensionally cultured cells have more physiologically relevant functions than two‐dimensionally cultured cells. Cells are three‐dimensionally surrounded by the extracellular matrix (ECM) in complex in vivo microenvironments and interact with the ECM and neighboring cells. Therefore, replicating the ECM environment is key to the successful cell culture models. Various natural and synthetic hydrogels have been used to mimic ECM environments based on their physical, chemical, and biological characteristics, such as biocompatibility, biodegradability, and biochemical functional groups. Because of these characteristics, hydrogels have been combined with microtechnologies and used in organ‐on‐a‐chip applications to more closely recapitulate the in vivo microenvironment. Therefore, appropriate hydrogels should be selected depending on the cell types and applications. The porosity of the selected hydrogel should be controlled to facilitate the movement of nutrients and oxygen. In this review, we describe various types of hydrogels, external stimulation‐based gelation of hydrogels, and control of their porosity. Then, we introduce applications of hydrogels for organ‐on‐a‐chip. Last, we also discuss the challenges of hydrogel‐based three‐dimensional cell culture techniques and propose future directions. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:580–589, 2017     

Serum concentrations of insulin‐like growth factor‐i and insulin‐like growth factor binding protein‐2 and ‐3 in eight hoofstock species

The somatotropic axis, which includes growth hormone, insulin‐like growth factor (IGF)‐I, and IGF binding proteins (IGFBP), is involved in the regulation of growth and metabolism. Measures of the somatotropic axis can be predictive of nutritional status and growth rate that can be utilized to identify nutritional status of individual animals. Before the somatotropic axis can be a predictive tool, concentrations of hormones of the somatotropic axis need to be established in healthy individuals. To begin to establish these data, we quantified IGF‐I, IGFBP‐2, and IGFBP‐3 in males and females of eight threatened hoofstock species at various ages. Opportunistic blood samples were collected from Bos javanicus (Java banteng), Tragelaphus eurycerus isaaci (bongo), Gazella dama ruficollis (addra gazelle), Taurotragus derbianus gigas (giant eland), Kobus megaceros (Nile lechwe), Hippotragus equines cottoni (roan antelope), Ceratotherium simum simum (white rhinoceros), and Elephas maximus (Asian elephant). Serum IGF‐I and IGFBPs were determined by radioimmunoassay and ligand blot, respectively. Generally, IGF‐I and IGFBP‐3 were greater in males, and IGFBP‐2 was greater in females. In banteng (P = 0.08) and male Nile lechwe (P<0.05), IGF‐I increased with age, but decreased in rhinoceros (P = 0.07) and female Nile lechwe (P<0.05). In banteng, IGFBP‐3 was greater (P<0.01) in males. In elephants (P<0.05) and antelope (P = 0.08), IGFBP‐2 were greater in females. Determination of concentrations of hormones in the somatotropic axis in healthy animals makes it possible to develop models that can identify the nutritional status of these threatened hoofstock species. Zoo Biol 30:275–284, 2011. © 2010 Wiley‐Liss, Inc.