scholarly journals Structural changes of protein antigens due to adsorption onto and release from aluminium hydroxide using FTIR–ATR

2007 ◽  
Vol 21 (4) ◽  
pp. 211-226 ◽  
Author(s):  
Yiwu Zheng ◽  
Xuxin Lai ◽  
Henrik Ipsen ◽  
Jørgen Nedergaard Larsen ◽  
Henning Løwenstein ◽  
...  
Keyword(s):  
Immune Response ◽  
Aluminium Hydroxide ◽  
Structural Changes ◽  
Structural Integrity ◽  
Structural Information ◽  
Cd Spectroscopy ◽  
Attenuated Total Reflection ◽  
Protein Antigens ◽  
Recovery Curves ◽  
Atr Spectroscopy

Structural integrity of antigens upon adsorption and release is not only important for investigating vaccine immunogenicity, but also for the epitope specificity of the resulting immune response and hence therapeutic efficacy. Moreover, the structural information is also important for understanding the mechanism of how adjuvants can enhance the immune response. However, little is known about an antigen's structure when it is adsorbed on and subsequently released from aluminium adjuvants. In this study, the structures of two protein antigens, bovine serum albumin and β-lactoglobulin, were investigated using Fourier transform infrared–attenuated total reflection (FTIR–ATR) spectroscopy. The secondary structures of both model antigens change when adsorbed to aluminium hydroxide. The structural perturbation depends on the amount of adsorbed protein. Maximal adsorption gives a more native-like structure. This may indicate that protein is adsorbed in different manners depending on the concentration. The adsorbed antigens are released using phosphate buffer pH 7.4 (PB). The recovery is approximate 80% after 40 min in the presence of PB. The recovery curves of both proteins also indicate two different adsorption modes. FTIR–ATR and circular dichroism (CD) spectroscopy yield similar results suggesting that the adsorbed antigens refold to their native-like state after release.

scholarly journals The structural stability of protein antigens adsorbed by aluminium hydroxide in comparison to the antigens in solutions

2007 ◽  
Vol 21 (5-6) ◽  
pp. 257-268 ◽  
Author(s):  
Yiwu Zheng ◽  
Xuxin Lai ◽  
Henrik Ipsen ◽  
Jørgen Nedergaard Larsen ◽  
Henning Løwenstein ◽  
...  
Keyword(s):  
Fourier Transform ◽  
Structural Stability ◽  
Aluminium Hydroxide ◽  
Storage Temperature ◽  
Total Reflection ◽  
Attenuated Total Reflection ◽  
Protein Antigens ◽  
Adsorbed Protein ◽  
Vaccine Immunogenicity ◽  
Atr Spectroscopy

It is believed that antigens should be adsorbed onto adjuvants in vaccines. The adsorption-modified structure of antigens is important to understand the mechanism of adjuvants and vaccine immunogenicity. The structural stability of antigens is of major importance. The changes in structure can be induced by degradation and/or increase of storage temperature. In this study the structural stability of two model antigens, bovine serum albumin (BSA) andβ-lactoglobulin (BLG) were compared when they were adsorbed onto aluminium hydroxide and when they were in solutions using Fourier transform infrared – attenuated total reflection (FTIR-ATR) spectroscopy. The structural stability of these two proteins was studied at different temperature and during storages. The present results showed that the structure of antigens can be stabilized by adsorption onto aluminium hydroxide. Non-adsorbed protein antigens present in vaccines may facilitate the degradation of the vaccine.

scholarly journals Structural analysis of proteins by isotope-edited FTIR spectroscopy

2010 ◽  
Vol 24 (1-2) ◽  
pp. 37-43 ◽  
Author(s):  
Suren A. Tatulian
Keyword(s):  
Structural Analysis ◽  
Ftir Spectroscopy ◽  
Structural Changes ◽  
Isotope Labeling ◽  
Structural Information ◽  
Attenuated Total Reflection ◽  
Site Specific ◽  
Segmental Isotope Labeling ◽  
Protein Membrane

Structure determination of multidomain proteins or protein–membrane complexes is one of the most challenging tasks in modern structural biology. High-resolution techniques, like NMR or X-ray crystallography, are limited to molecules of moderate size or those that can be crystallized easily. Both methods encounter serious technical obstacles in structural analysis of protein–membrane systems. This work describes an emerging biophysical technique that combines segmental isotope labeling of proteins with Fourier transform infrared (FTIR) spectroscopy, which provides site-specific structural information on proteins and allows structural characterization of protein–membrane complexes. Labeling of a segment of the protein with13C results in infrared spectral resolution of the labeled and unlabeled parts and thus allows identification of structural changes in specific domains/segments of the protein that accompany functional transitions. Segmental isotope labeling also allows determination of the precise configuration of protein–membrane complexes by polarized attenuated total reflection FTIR (ATR–FTIR) spectroscopy. These new developments offer solutions to functionally important site-specific structural changes in proteins and protein–membrane complexes that are hard to approach using conventional methods.

scholarly journals Conformational dynamics of androgen receptors bound to agonists and antagonists

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hyo Jin Gim ◽  
Jiyong Park ◽  
Michael E. Jung ◽  
K. N. Houk
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
Structural Integrity ◽  
Structural Information ◽  
Close Contact ◽  
Conformational Dynamics ◽  
Principal Component ◽  
Binding Pocket ◽  
Structural Basis ◽  
Accelerated Molecular Dynamics

AbstractThe androgen receptor (AR) is critical in the progression of prostate cancer (PCa). Small molecule antagonists that bind to the ligand binding domain (LBD) of the AR have been successful in treating PCa. However, the structural basis by which the AR antagonists manifest their therapeutic efficacy remains unclear, due to the lack of detailed structural information of the AR bound to the antagonists. We have performed accelerated molecular dynamics (aMD) simulations of LBDs bound to a set of ligands including a natural substrate (dihydrotestosterone), an agonist (RU59063) and three antagonists (bicalutamide, enzalutamide and apalutamide) as well as in the absence of ligand (apo). We show that the binding of AR antagonists at the substrate binding pocket alter the dynamic fluctuations of H12, thereby disrupting the structural integrity of the agonistic conformation of AR. Two antagonists, enzalutamide and apalutamide, induce considerable structural changes to the agonist conformation of LBD, when bound close to H12 of AR LBD. When the antagonists bind to the pocket with different orientations having close contact with H11, no significant conformational changes were observed, suggesting the AR remains in the functionally activated (agonistic) state. The simulations on a drug resistance mutant F876L bound to enzalutamide demonstrated that the mutation stabilizes the agonistic conformation of AR LBD, which compromises the efficacy of the antagonists. Principal component analysis (PCA) of the structural fluctuations shows that the binding of enzalutamide and apalutamide induce conformational fluctuations in the AR, which are markedly different from those caused by the agonist as well as another antagonist, bicalutamide. These fluctuations could only be observed with the use of aMD.

Individual differences in white and grey matter structure associated with verbal habits of thought

2019 ◽  
Author(s):  
Justin C. Hayes ◽  
Katherine L Alfred ◽  
Rachel Pizzie ◽  
Joshua S. Cetron ◽  
David J. M. Kraemer
Keyword(s):  
Individual Differences ◽  
White Matter ◽  
Cognitive Processing ◽  
Grey Matter ◽  
Structural Changes ◽  
Structural Integrity ◽  
Diffusion Tensor ◽  
Self Report ◽  
White Matter Tracts

Modality specific encoding habits account for a significant portion of individual differences reflected in functional activation during cognitive processing. Yet, little is known about how these habits of thought influence long-term structural changes in the brain. Traditionally, habits of thought have been assessed using self-report questionnaires such as the visualizer-verbalizer questionnaire. Here, rather than relying on subjective reports, we measured habits of thought using a novel behavioral task assessing attentional biases toward picture and word stimuli. Hypothesizing that verbal habits of thought are reflected in the structural integrity of white matter tracts and cortical regions of interest, we used diffusion tensor imaging and volumetric analyses to assess this prediction. Using a whole-brain approach, we show that word bias is associated with increased volume in several bilateral language regions, in both white and grey matter parcels. Additionally, connectivity within white matter tracts within an a priori speech production network increased as a function of word bias. These results demonstrate long-term structural and morphological differences associated with verbal habits of thought.

scholarly journals A graph-based algorithm for detecting rigid domains in protein structures

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Truong Khanh Linh Dang ◽  
Thach Nguyen ◽  
Michael Habeck ◽  
Mehmet Gültas ◽  
Stephan Waack
Keyword(s):  
Structural Changes ◽  
Viterbi Algorithm ◽  
Structural Information ◽  
Line Graph ◽  
Clustering Algorithms ◽  
Protein Structures ◽  
Alternative Methods ◽  
Structural Transitions ◽  
Tuning Parameters ◽  
Conformational Ensembles

Abstract Background Conformational transitions are implicated in the biological function of many proteins. Structural changes in proteins can be described approximately as the relative movement of rigid domains against each other. Despite previous efforts, there is a need to develop new domain segmentation algorithms that are capable of analysing the entire structure database efficiently and do not require the choice of protein-dependent tuning parameters such as the number of rigid domains. Results We develop a graph-based method for detecting rigid domains in proteins. Structural information from multiple conformational states is represented by a graph whose nodes correspond to amino acids. Graph clustering algorithms allow us to reduce the graph and run the Viterbi algorithm on the associated line graph to obtain a segmentation of the input structures into rigid domains. In contrast to many alternative methods, our approach does not require knowledge about the number of rigid domains. Moreover, we identified default values for the algorithmic parameters that are suitable for a large number of conformational ensembles. We test our algorithm on examples from the DynDom database and illustrate our method on various challenging systems whose structural transitions have been studied extensively. Conclusions The results strongly suggest that our graph-based algorithm forms a novel framework to characterize structural transitions in proteins via detecting their rigid domains. The web server is available at http://azifi.tz.agrar.uni-goettingen.de/webservice/.

Diffusion Measurements Using FT-IR ATR Spectroscopy: Lubricant Diffusion in Polypropylene

2002 ◽  
Vol 56 (4) ◽  
pp. 509-514 ◽  
Author(s):  
Xiaohua Yi ◽  
Karen Nerbonne ◽  
John Pellegrino
Keyword(s):  
Current Model ◽  
Mineral Oil ◽  
Attenuated Total Reflection ◽  
Lubricant Layer ◽  
Polymer Interfaces ◽  
Time Resolved ◽  
Polymer Sample ◽  
Ft Ir ◽  
Atr Spectroscopy ◽  
Poly Propylene

We present an experimental method for measuring diffusion of lubricants (or any highly viscous fluid) in polymers using Fourier transform infrared (FT-IR) attenuated total reflection (ATR) spectroscopy. Unlike the conventional FT-IR ATR diffusion measurement, in which a polymer sample is sandwiched between the penetrant and an internal reflection element (IRE), in this method, a thin layer of penetrant (for example, a lubricant) is sandwiched between the IRE and the polymer sample. This allows accurate control and measurement of the thickness of the lubricant layer, which, in turn, facilitates subsequent data analysis. The diffusion is studied by monitoring the time-resolved change in absorbance of either a unique polymer or penetrant band. A feature of this new method is that it can provide an estimate of solubility, as well as an estimate of the diffusivity of the penetrant in the polymer. Using this method, we studied the diffusion of mineral oil and a commercial fluorocarbon ether lubricant (Krytox® 143AC‡) in poly(propylene) (PP) film at room temperature. The experimental data was modeled using a Fickian model with impermeable and saturated boundary conditions applied at the IRE/lubricant and lubricant/polymer interfaces, respectively. The diffusivity and solubility of mineral oil in PP were found to be 1.34 ± 0.35 (×10−10) cm2/s and 0.77 ± 0.13 (×10−2) g/g of PP, respectively. The current model was unable to quantitatively describe the diffusion of the Krytox® 143AC in the PP, possibly due to excessive swelling.

Identifying and Evaluating Anomalous Structural Change-based Nodes in Generalized Dynamic Social Networks

2021 ◽  
Vol 15 (4) ◽  
pp. 1-22
Author(s):  
Huan Wang ◽  
Chunming Qiao ◽  
Xuan Guo ◽  
Lei Fang ◽  
Ying Sha ◽  
...  
Keyword(s):  
Social Networks ◽  
Structural Change ◽  
Structural Changes ◽  
Structural Information ◽  
Similarity Index ◽  
Dynamic Social Network ◽  
Dynamic Social Networks ◽  
Micro Level ◽  
Anomaly Analysis ◽  
Similarity Method

Recently, dynamic social network research has attracted a great amount of attention, especially in the area of anomaly analysis that analyzes the anomalous change in the evolution of dynamic social networks. However, most of the current research focused on anomaly analysis of the macro representation of dynamic social networks and failed to analyze the nodes that have anomalous structural changes at a micro level. To identify and evaluate anomalous structural change-based nodes in generalized dynamic social networks that only have limited structural information, this research considers undirected and unweighted graphs and develops a multiple-neighbor superposition similarity method ( ), which mainly consists of a multiple-neighbor range algorithm ( ) and a superposition similarity fluctuation algorithm ( ). introduces observation nodes, characterizes the structural similarities of nodes within multiple-neighbor ranges, and proposes a new multiple-neighbor similarity index on the basis of extensional similarity indices. Subsequently, maximally reflects the structural change of each node, using a new superposition similarity fluctuation index from the perspective of diverse multiple-neighbor similarities. As a result, based on and , not only identifies anomalous structural change-based nodes by detecting the anomalous structural changes of nodes but also evaluates their anomalous degrees by quantifying these changes. Results obtained by comparing with state-of-the-art methods via extensive experiments show that can accurately identify anomalous structural change-based nodes and evaluate their anomalous degrees well.

Model Optimization and Stability of Hemoglobin Analysis in Human Soluble Blood Samples by FTIR/ATR Spectroscopy

2011 ◽  
Vol 55-57 ◽  
pp. 1168-1171
Author(s):  
Tao Pan ◽  
Ai Hong Peng ◽  
Wen Jie Huang
Keyword(s):  
Signal To Noise Ratio ◽  
Attenuated Total Reflection ◽  
Partial Least Square ◽  
Least Square ◽  
Model Optimization ◽  
Optimal Model ◽  
Blood Samples ◽  
Quantification Method ◽  
Atr Spectroscopy ◽  
Pls Method

Using Fourier transform infrared spectroscopy (FTIR), attenuated total reflection (ATR) technology and partial least square (PLS) method, the rapid quantification method of hemoglobin (HGB) in human soluble blood samples was established. Based on the distribution of samples’ HGB chemical value and absorbance on 1543 cm-1 which had the highest signal to noise ratio for HGB, all samples were divided into calibration set and prediction set for 50 times. PLS models were established for all divisions, based on the average data RMSEPAve, the stable optimal model was selected, the corresponding PLS factor, RMSEPAve and RP,Ave were 2, 6.81 g/L and 0.943 respectively.

Application Of Systems With Total Internal Reflection At Novosibirsk Free Electron Laser For Spectroscopy In The Terahertz Range

2016 ◽  
Vol 11 (3) ◽  
pp. 72-82
Author(s):  
Vasily Gerasimov ◽  
Elvira Grigorieva ◽  
Boris Knyazev ◽  
Yuliya Choporova
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Quantum Cascade Lasers ◽  
Attenuated Total Reflection ◽  
Terahertz Range ◽  
Optical Systems ◽  
Early Diagnosis Of Cancer ◽  
Infrared Spectral ◽  
Atr Spectroscopy ◽  
Spectral Ranges

Attenuated total reflection (ATR) spectroscopy is widely used in the visible and infrared spectral ranges. Progress in the development of laboratory scale monochromatic sources of terahertz radiation, such as quantum cascade lasers, suggests that in the near future this kind of spectrometers will be widely spread in the terahertz range. For this reason, the development of ATR based methods and devices is highly relevant. In this paper, we discuss the features of the use of ATR spectroscopy in the terahertz range, and describe some of the optical systems, designed for experiments at the Novosibirsk free electron laser (NovoFEL). We show that in the terahertz range the ATR spectroscopy has a number of significant advantages over the absorption spectroscopy. As an example, we are discussing the possibility of using terahertz polarimetry to develop a method for early diagnosis of cancer via the detection of left-handed to right-handed polysaccharide enantiomers ratio. Spectra of selected polysaccharides were recorded with a standard Fourier spectrometer using developed by us an ATR unit. The possibility of studying the polarization characteristics of polysaccharides in aqueous solutions using spectrally selective polarimeter with the NovoFEL as a tunable radiation source was demonstrated.

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