scholarly journals The Structure of Amyloid Versus the Structure of Globular Proteins

2020 ◽  
Vol 21 (13) ◽  
pp. 4683 ◽  
Author(s):  
Piotr Fabian ◽  
Mateusz Banach ◽  
Katarzyna Stapor ◽  
Leszek Konieczny ◽  
Magdalena Ptak-Kaczor ◽  
...  
Keyword(s):  
Gaussian Distribution ◽  
Experimental Studies ◽  
Data Bank ◽  
Globular Proteins ◽  
Hydrophobic Core ◽  
Single Chain ◽  
Spherical Micelle ◽  
Globular Structure ◽  
A Chain ◽  
High Level

The issue of changing the structure of globular proteins into an amyloid form is in the focus of researchers' attention. Numerous experimental studies are carried out, and mathematical models to define the essence of amyloid transformation are sought. The present work focuses on the issue of the hydrophobic core structure in amyloids. The form of ordering the hydrophobic core in globular proteins is described by a 3D Gaussian distribution analog to the distribution of hydrophobicity in a spherical micelle. Amyloid fibril is a ribbon-like micelle made up of numerous individual chains, each representing a flat structure. The distribution of hydrophobicity within a single chain included in the fibril describes the 2D Gaussian distribution. Such a description expresses the location of polar residues on a circle with a center with a high level of hydrophobicity. The presence of this type of order in the amyloid forms available in Preotin Data Bank (PDB) (both in proto- and superfibrils) is demonstrated in the present work. In this system, it can be assumed that the amyloid transformation is a chain transition from 3D Gauss ordering to 2D Gauss ordering. This means changing the globular structure to a ribbon-like structure. This observation can provide a simple mathematical model for simulating the amyloid transformation of proteins.

scholarly journals The Amyloid as a Ribbon-Like Micelle in Contrast to Spherical Micelles Represented by Globular Proteins

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4395 ◽  
Author(s):  
Mateusz Banach ◽  
Leszek Konieczny ◽  
Irena Roterman
Keyword(s):  
Gaussian Distribution ◽  
Amyloid Fibrils ◽  
Data Bank ◽  
Globular Proteins ◽  
Structural Pattern ◽  
Hydrophobic Residues ◽  
Aqueous Solvent ◽  
Conformational Diversity ◽  
Spherical Micelles ◽  
Hydrophobic Cores

Selected amyloid structures available in the Protein Data Bank have been subjected to a comparative analysis. Classification is based on the distribution of hydrophobicity in amyloids that differ with respect to sequence, chain length, the distribution of beta folds, protofibril structure, and the arrangement of protofibrils in each superfibril. The study set includes the following amyloids: Aβ (1–42), which is listed as Aβ (15–40) and carries the D23N mutation, and Aβ (11–42) and Aβ (1–40), both of which carry the E22Δ mutation, tau amyloid, and α-synuclein. Based on the fuzzy oil drop model (FOD), we determined that, despite their conformational diversity, all presented amyloids adopt a similar structural pattern that can be described as a ribbon-like micelle. The same model, when applied to globular proteins, results in structures referred to as “globular micelles,” emerging as a result of interactions between the proteins’ constituent residues and the aqueous solvent. Due to their composition, amyloids are unable to attain entropically favorable globular forms and instead attempt to limit contact between hydrophobic residues and water by producing elongated structures. Such structures typically contain quasi hydrophobic cores that stretch along the fibril’s long axis. Similar properties are commonly found in ribbon-like micelles, with alternating bands of high and low hydrophobicity emerging as the fibrils increase in length. Thus, while globular proteins are generally consistent with a 3D Gaussian distribution of hydrophobicity, the distribution instead conforms to a 2D Gaussian distribution in amyloid fibrils.

scholarly journals Filamentous Aggregates of Tau Proteins Fulfil Standard Amyloid Criteria

2018 ◽  
Author(s):  
Dawid Dułak ◽  
Małgorzata Gadzała ◽  
Mateusz Banach ◽  
Magdalena Ptak ◽  
Zdzisław Wisniowski ◽  
...  
Keyword(s):  
Tau Protein ◽  
Amyloid Fibrils ◽  
Globular Proteins ◽  
Tau Proteins ◽  
Hydrophobic Core ◽  
Linear Structures ◽  
Spherical Micelle ◽  
Cylindrical Structure ◽  
Limit Form

Abnormal filamentous aggregates formed by tangled tau protein turn out to be classic amyloid fibrils, meeting all criteria defined under the fuzzy oil drop model in the context of amyloid characterization. The model recognizes amyloids as linear structures where local hydrophobicity minima and maxima propagate in an alternating manner along the fibril’s long axis. This distribution of hydrophobicity differs greatly from the classic monocentric hydrophobic core observed in globular proteins. Rather than becoming a globule, the amyloid instead forms a ribbonlike (or cylindrical) structure, which can be thought of as a distorted spherical micelle, which in limit form appears to be the ribbon-like micelle.

scholarly journals Divergence Entropy-Based Evaluation of Hydrophobic Core in Aggressive and Resistant Forms of Transthyretin

Entropy ◽  
2021 ◽  
Vol 23 (4) ◽  
pp. 458
Author(s):  
Mateusz Banach ◽  
Katarzyna Stapor ◽  
Piotr Fabian ◽  
Leszek Konieczny ◽  
Irena Roterman
Keyword(s):  
Tertiary Structure ◽  
Early Stage ◽  
Intermediate Stage ◽  
Transformation Process ◽  
Hydrophobic Core ◽  
Spherical Micelle ◽  
Globular Structure ◽  
Folding Process ◽  
Decisive Importance ◽  
The Status

The two forms of transthyretin differing slightly in the tertiary structure, despite the presence of five mutations, show radically different properties in terms of susceptibility to the amyloid transformation process. These two forms of transthyretin are the object of analysis. The search for the sources of these differences was carried out by means of a comparative analysis of the structure of these molecules in their native and early intermediate stage forms in the folding process. The criterion for assessing the degree of similarity and differences is the status of the hydrophobic core. The comparison of the level of arrangement of the hydrophobic core and its initial stages is possible thanks to the application of divergence entropy for the early intermediate stage and for the final forms. It was shown that the minimal differences observed in the structure of the hydrophobic core of the forms available in PDB, turned out to be significantly different in the early stage (ES) structure in folding process. The determined values of divergence entropy for both ES forms indicate the presence of the seed of hydrophobic core only in the form resistant to amyloid transformation. In the form of aggressively undergoing amyloid transformation, the structure lacking such a seed is revealed, being a stretched one with a high content of β-type structure. In the discussed case, the active presence of water in the structural transformation of proteins expressed in the fuzzy oil drop model (FOD) is of decisive importance for the generation of the final protein structure. It has been shown that the resistant form tends to generate a centric hydrophobic core with the possibility of creating a globular structure, i.e. a spherical micelle-like form. The aggressively transforming form reveals in the structure of its early intermediate, a tendency to form the ribbon-like micelle as observed in amyloid.

LIPOPOLYSACCHARIDE-SENSITIVE SERINE-PROTEASE ZYMOGEN (FACTOR C) OF LIMULUS HEMOCYTES: IDENTIFICATION AND ALIGNMENT OF PROTEOLYTIC FRAGMENTS PRODUCED DURING THE ACTIVATION SHOW THAT IT IS A NOVEL TYPE OF SERINE-PROTEASE

1987 ◽  
Author(s):  
F Tokunaga ◽  
T Miyata ◽  
T Nakamura ◽  
T Morita ◽  
S Iwanaga
Keyword(s):  
Serine Protease ◽  
Heavy Chain ◽  
Light Chain ◽  
Interleukin 2 ◽  
Coagulation Factor ◽  
Clotting Factor ◽  
Single Chain ◽  
Terminal Sequence ◽  
A Chain ◽  
Factor C

Limulus clotting factor, factor C, is a lipopolysaccharide (LPS)-sensitive serine-protease zymogen present in the hemocytes. It is a two-chain glycoprotein (M.W. = 123,000) composed of a heavy chain (M.W. = 80,000) and a light chain (M.W. = 43,000) T. Nakamura et al. (1986) Eur. J. Biochem. 154, 511-521 .On further studies of this zymogen, a single-chain factor C (M.W. = 123,000) was identified by Western blotting technique. The heavy chain had an NH2-terminal sequence of Ser-Gly-Val-Asp-, which was consistent with the NH2-terminal sequence of the single-chain factor C, indicating that the heavy chain is located in the NH2-terminal part of the zymogen. The light chain had an NH22-terminal sequence of Ser-Ser-Gln-Pro-. Incubation of the two-chain zymogen with LPS resulted in the cleavage of a Phe-Ile bond between residues 72 and 73 of the light chain. Concomitant with this cleavage, the A (72.amino acids) and B chains derived from the light chain was formed. The complete amino acid sequence of the A chain was determined by automated Edman degradation. The A chain contained a typical segment which is similar structuraly to those a family of repeats in human β2 -glycoprotein I, complement factors B, Clr, Cls, H, C4b-binding protein, 02, coagulation factor XIII b subunit, haptoglobin a chain, and interleukin 2 receptor. The NH2-terminal sequence of the B chain was Ile-Trp-Asn-Gly-. This chain contained the serine-active site sequence of -ASP-Ala-Cys-Ser-Gly-Asp-SER-Gly-Gly-Pro-.These results indicate that limulus factor C exists in the hemocytes in a single-chain zymogen form and is converted to an active serine-protease by hydrolysis of a specific Phe-Ile peptide bond. The correlation of limulus factor C and mammalian complement proteins was also suggested.

Impurity leakage and radiative cooling in the first nitrogen and neon seeding study in the slot divertor at DIII-D

2021 ◽  
Author(s):  
Livia Casali ◽  
David Eldon ◽  
Adam G McLean ◽  
Tom H Osborne ◽  
Anthony W Leonard ◽  
...  
Keyword(s):  
Experimental Studies ◽  
Mean Free Path ◽  
Flow Reversal ◽  
Momentum Balance ◽  
Ionization Source ◽  
Power Flux ◽  
Impurity Transport ◽  
Plasma Drifts ◽  
High Level ◽  
The Impact

Abstract A comparative study of nitrogen versus neon has been carried out to analyze the impact of the two radiative species on power dissipation, SOL impurity distribution, divertor and pedestal characteristics. The experimental results show that N remains compressed in the divertor, thereby providing high radiative losses without affecting the pedestal profiles and displacing carbon as dominant radiator. Neon, instead, radiates more upstream than N thus reducing the power flux through the separatrix leading to a reduced ELM frequency and compression in the divertor. A significant amount of neon is measured in the plasma core leading to a steeper density gradient. The different behaviour between the two impurities is confirmed by SOLPS-ITER modelling which for the first time at DIII-D includes multiple impurity species and a treatment of full drifts, currents and neutral-neutral collisions. The impurity transport in the SOL is studied in terms of the parallel momentum balance showing that N is mostly retained in the divertor whereas Ne leaks out consistent with its higher ionization potential and longer mean free path. This is also in agreement with the enrichment factor calculations which indicate lower divertor enrichment for neon. The strong ionization source characterizing the SAS divertor causes a reversal of the main ions and impurity flows. The flow reversal together with plasma drifts and the effect of the thermal force contribute significantly in the shift of the impurity stagnation point affecting impurity leakage. This work provides a demonstration of the impurity leakage mechanism in a closed divertor structure and the consequent impact on pedestal. Since carbon is an intrinsic radiator at DIII-D, in this paper we have also demonstrated the different role of carbon in the N vs Ne seeded cases both in the experiments and in the numerical modeling. Carbon contributes more when neon seeding is injected compared to when nitrogen is used. Finally, the results highlight the importance of accompanying experimental studies with numerical modelling of plasma flows, drifts and ionization profile to determine the details of the SOL impurity transport as the latter may vary with changes in divertor regime and geometry. In the cases presented here, plasma drifts and flow reversal caused by high level of closure in the slot upper divertor at DIII-D play an important role in the underlined mechanism.

The York-Arup cable experiments: Implications for the fire design of cable-supported bridges

2021 ◽  
Author(s):  
Benjamin Nicoletta ◽  
John Gales ◽  
Panagiotis Kotsovinos
Keyword(s):  
Thermal Strain ◽  
Experimental Studies ◽  
Thermal Response ◽  
Structural Response ◽  
Fire Performance ◽  
Stay Cable ◽  
Stay Cables ◽  
Bridge Structures ◽  
Recent Trends ◽  
High Level

<p>Recent trends towards performance-based fire designs for complex and critical structures have posed questions about the fire resilience of bridge infrastructure. There are little-to-no code requirements for bridge fire resistance and practitioner guidance on the subject is limited. Research on the fire performance of cable-supported bridge structures is scarce and knowledge gaps persist that inhibit more informed fire protection designs in a variety of bridge types. There have been few numerical or experimental studies that investigate the fire performance of steel stay-cables for use in cable-supported bridges. The thermal response of these members is critical as cable systems are highly dependent on the response of individual members, such as in the case of an anchor cable for example. The study herein examines the thermal response of several varieties of unloaded steel- stay cable during exposure to a non-standard methanol pool fire and the implications for the structural response of a cable-supported bridge. Experimental thermal strain data from fire tests of various stay-cables is used to inform high-level insights for the global response of a cable-supported bridge. Namely, the effects of cable thermal expansion on the overall cable system is approximated.</p>

scholarly journals Integration of Blockchain Technology in IoT for High Level Security

2019 ◽  
Vol 8 (10) ◽  
pp. 491-497
Keyword(s):  
Radio Frequency Identification ◽  
Humidity Sensor ◽  
Raspberry Pi ◽  
Distributed Network ◽  
Peer Communication ◽  
Blockchain Technology ◽  
Frequency Identification ◽  
A Chain ◽  
High Level ◽  
Machine Communication

IoT (Internet of Things) made headway from Machine to Machine communication without human intrusion for number of machines to connect with the aid of network. There is esteem; by 2020 there will be 26 times more connected things than people. Hence, the concern of security rises along with the high installments. The BlockChain Technology takes place of all central entities, which is peer to peer communication with the distributed network. In this paper, two Arduino boards as nodes and a Raspberry Pi as server are to be configured to connect to the Wi-Fi using ESP8266(node mc). To make data transmission from the two nodes to server, integration of temperature and humidity sensor in one node and RFID (Radio Frequency Identification) reader in other node is to be done. Data should be in the form of blocks and integration of data is in the form of a chain, forming it a Blockchain. All the blocks are linked in the chain manner of which the current hash of the previous block must match with the previous hash of the next block. Then only the blocks of data are secured. While receiving data every time from nodes to server, the previous hash is to be checked such that the arrival of the information is being verified to know if it’s really genuine. If the cryptographic hash does not match then data manipulation is happened. So, in this paper, we will see, along with how practically the security is highly offered by the blockchain technology and how can we easily identify if the data has been tampered along the way it reaches to us. Henceforth, we will found a way of application to secure our IoT data without any regrets in this paper.

A Solid-State NMR Approach to Structure Determination of Membrane-Associated Peptides and Proteins

1997 ◽  
Author(s):  
S.J. Opella ◽  
L.E. Chirlian
Keyword(s):  
Nmr Spectroscopy ◽  
Membrane Proteins ◽  
Structural Biology ◽  
Experimental Studies ◽  
Globular Proteins ◽  
Biological Properties ◽  
Cellular Functions ◽  
X Ray ◽  
X Ray Crystallography ◽  
Form And Function

Structural biology relies on detailed descriptions of the three-dimensional structures of peptides, proteins, and other biopolymers to explain the form and function of biological systems ranging in complexity from individual molecules to entire organisms. NMR spectroscopy and X-ray crystallography, in combination with several types of calculations, provide the required structural information. In recent years, the structures of several hundred proteins have been determined by one or both of these experimental methods. However, since the protein molecules must either reorient rapidly in samples for multidimensional solution NMR spectroscopy or form high quality single crystals in samples for X-ray crystallography, nearly all of the structures determined up to now have been of the soluble, globular proteins that are found in the cytoplasm and periplasmof cells and fortuitously have these favorable properties. Since only a minority of biological properties are expressed by globular proteins, and proteins, in general, have evolved in order to express specific functions rather than act as samples for experimental studies, there are other classes of proteins whose structures are currently unknown but are of keen interest in structural biology. More than half of all proteins appear to be associated with membranes, and many cellular functions are expressed by proteins in other types of supramolecular complexes with nucleic acids, carbohydrates, or other proteins. The interest in the structures of membrane proteins, structural proteins, and proteins in complexes provides many opportunities for the further development and application of NMR spectroscopy. Our understanding of polypeptides associated with lipids in membranes, in particular, is primitive, especially compared to that for globular proteins. This is largely a consequence of the experimental difficulties encountered in their study by conventional NMR and X-ray approaches. Fortunately, the principal features of two major classes of membrane proteins have been identified from studies of several tractable examples. Bacteriorhodopsin (Henderson et al., 1990), the subunits of the photosynthetic reaction center (Deisenhofer et al., 1985), and filamentous bacteriophage coat proteins (Shon et al., 1991; McDonnell et al., 1993) have all been shown to have long transmembrane hydrophobic helices, shorter amphipathic bridging helices in the plane of the bilayers, both structured and mobile loops connecting the helices, and mobile N- and C-terminal regions.

scholarly journals New chemical scheme for giant planet thermochemistry

2020 ◽  
Vol 634 ◽  
pp. A78 ◽  
Author(s):  
O. Venot ◽  
T. Cavalié ◽  
R. Bounaceur ◽  
P. Tremblin ◽  
L. Brouillard ◽  
...  
Keyword(s):  
Experimental Studies ◽  
Giant Planet ◽  
Brown Dwarfs ◽  
Planetary Atmospheres ◽  
Atmospheric Composition ◽  
Planetary Formation ◽  
Hot Jupiters ◽  
Chemical Scheme ◽  
High Level ◽  
Kinetics Of

Context. Several chemical networks have been developed to study warm (exo)planetary atmospheres. The kinetics of the reactions related to the methanol chemistry included in these schemes have been questioned. Aims. The goal of this paper is to update the methanol chemistry for such chemical networks based on recent publications in the combustion literature. We also aim to study the consequences of this update on the atmospheric compositions of (exo)planetary atmospheres and brown dwarfs. Methods. We performed an extensive review of combustion experimental studies and revisited the sub-mechanism describing methanol combustion in a scheme published in 2012. The updated scheme involves 108 species linked by a total of 1906 reactions. We then applied our 1D kinetic model with this new scheme to the case studies HD 209458b, HD 189733b, GJ 436b, GJ 1214b, ULAS J1335+11, Uranus, and Neptune; we compared these results with those obtained with the former scheme. Results. The update of the scheme has a negligible impact on the atmospheres of hot Jupiters. However, the atmospheric composition of warm Neptunes and brown dwarfs is modified sufficiently to impact observational spectra in the wavelength range in which James Webb Space Telescope will operate. Concerning Uranus and Neptune, the update of the chemical scheme modifies the abundance of CO and thus impacts the deep oxygen abundance required to reproduce the observational data. For future 3D kinetics models, we also derived a reduced scheme containing 44 species and 582 reactions. Conclusions. Chemical schemes should be regularly updated to maintain a high level of reliability on the results of kinetic models and be able to improve our knowledge of planetary formation.

Objectives and Review of the International Milk Fluoridation Program

1995 ◽  
Vol 9 (2) ◽  
pp. 110-111 ◽  
Author(s):  
G.N. Pakhomo
Keyword(s):  
Dental Caries ◽  
National Level ◽  
Data Bank ◽  
Epidemiological Studies ◽  
Weighted Mean ◽  
Number Of Children ◽  
The World ◽  
Low Levels ◽  
High Level ◽  
Very High

The WHO Global Oral Data Bank (GODB) demonstrates wide varieties of dental caries levels. During the last 10 years, dental caries prevalence in many countries has decreased from very high and high to moderate and low levels. However, there also are countries where dental caries has increased from very low and low to a moderate level. In total in 1993, of the 158 countries for which the WHO GODB has data available, 16 countries indicate a very low level (69 - low, 53 - moderate, 17 - high), and only three a very high level of dental caries. Very high levels of dental caries have been recorded in Costa Rica, Jamaica, and Uruguay. All these data, based on the weighted mean of DMF in 12-year-old children, have been obtained from national surveys or collected from published papers on oral health surveys conducted in selected areas of the countries. Very often, these papers indicated an increase (or decrease) in dental caries in people living in different areas of a particular country; however, the DMF weighted mean at the national level is still without change. One of the most populated countries in the world, China, shows clear evidence from several recent epidemiological studies that the level of dental caries in the urban population is persistently increasing. Dental caries still remains one of the most common diseases affecting a substantial number of children and adults around the world. There is evidence that water or

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