scholarly journals Analysis of Protein Intramolecular and Solvent Bonding on Example of Major Synovial Fluid Component

2019 ◽  
Author(s):  
Krzysztof Domino ◽  
Damian Bełdowski ◽  
Adam Mazurkiewicz ◽  
Janusz Musiał ◽  
Małgorzata Słomion ◽  
...  
Keyword(s):  
Amino Acids ◽  
Synovial Fluid ◽  
Hydrogen Bonds ◽  
Power Spectra ◽  
Point Of View ◽  
Experimental Setting ◽  
Scaling Exponents ◽  
Fluid Component ◽  
Solvent Bonding ◽  
Pi Interactions

In this paper we review dynamics and roughness of bonds in proteins on example of albumin, that is important from the physiological point of view. We have performed computer simulations of albumin chain. Statistics were collected by performing many simulations realizations for each experimental setting. We concentrate on hydrogen bonds, cation-π and π- π interactions and NP contacts. Histograms of hydrogen bonds length are positively skewed in contrary to histograms of interactions and HP contacts that are negatively skewed. Scaling exponents of power spectra of energies of bonds / interactions /contacts are in range -0.2 to -0.5 and significantly differ between various hydrogen bonds or interactions. Varying scaling of such spectra can be used to classify between distinct bonds or contacts. Concerning particular amino-acids, largest amount of HBO H20 bonds are between Glutamate (GLU) amino-acids and water particle, while large amount of HBO bonds are formed with Lysine (LYS). For HP contacts the mayor role plays Phenylalanine (PHE) and Leucine (LEU) amino-acids. From decay curves HBO H2O bonds decays in fastest rate, while HBO bonds and HP contacts at slowest rate. We present as well decay curves of bonds formed by particular amino-acids, that gives interesting results.

scholarly journals On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 99
Author(s):  
Cristian Privat ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Jaime Rubio-Martínez
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Md Simulations ◽  
Point Of View ◽  
Conformational Space ◽  
Conformational Sampling ◽  
Protonation State ◽  
Constant Ph ◽  
Biochemical Systems ◽  
Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

scholarly journals Recuperative Amino Acids Separation through Cellulose Derivative Membranes with Microporous Polypropylene Fiber Matrix

Membranes ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 429
Author(s):  
Aurelia Cristina Nechifor ◽  
Andreia Pîrțac ◽  
Paul Constantin Albu ◽  
Alexandra Raluca Grosu ◽  
Florina Dumitru ◽  
...  
Keyword(s):  
Amino Acids ◽  
Cellulose Acetate ◽  
Polypropylene Fiber ◽  
Point Of View ◽  
Hydroxyethyl Cellulose ◽  
Separation Performance ◽  
Thermal Gravimetric Analyzer ◽  
Microfiltration Membranes ◽  
Ft Ir ◽  
Structural Point

The separation, concentration and transport of the amino acids through membranes have been continuously developed due to the multitude of interest amino acids of interest and the sources from which they must be recovered. At the same time, the types of membranes used in the sepa-ration of the amino acids are the most diverse: liquids, ion exchangers, inorganic, polymeric or composites. This paper addresses the recuperative separation of three amino acids (alanine, phe-nylalanine, and methionine) using membranes from cellulosic derivatives in polypropylene ma-trix. The microfiltration membranes (polypropylene hollow fibers) were impregnated with solu-tions of some cellulosic derivatives: cellulose acetate, 2-hydroxyethyl-cellulose, methyl 2-hydroxyethyl-celluloseand sodium carboxymethyl-cellulose. The obtained membranes were characterized in terms of the separation performance of the amino acids considered (retention, flux, and selectivity) and from a morphological and structural point of view: scanning electron microscopy (SEM), high resolution SEM (HR-SEM), Fourier transform infrared spectroscopy (FT-IR), energy dispersive spectroscopy (EDS) and thermal gravimetric analyzer (TGA). The re-sults obtained show that phenylalanine has the highest fluxes through all four types of mem-branes, followed by methionine and alanine. Of the four kinds of membrane, the most suitable for recuperative separation of the considered amino acids are those based on cellulose acetate and methyl 2-hydroxyethyl-cellulose.

scholarly journals Organotin(IV) selenate derivatives – Crystal structure of [{(Ph3Sn)2SeO4} ⋅ CH3OH] n

2021 ◽  
Vol 44 (1) ◽  
pp. 213-217
Author(s):  
Waly Diallo ◽  
Hélène Cattey ◽  
Laurent Plasseraud
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Point Of View ◽  
Intermolecular Hydrogen Bonds

Abstract Crystallization of [(Ph3Sn)2SeO4] ⋅ 1.5H2O in methanol leads to the formation of [{(Ph3Sn)2SeO4} ⋅ CH3OH] n (1) which constitutes a new specimen of organotin(IV) selenate derivatives. In the solid state, complex 1 is arranged in polymeric zig-zag chains, composed of alternating Ph3Sn and SeO4 groups. In addition, pendant Ph3Sn ⋅ CH3OH moieties are branched along chains according to a syndiotactic organization and via Sn-O-Se connections. From a supramolecular point of view, intermolecular hydrogen bonds established between the selenate groups (uncoordinated oxygen) and the hydroxyl functions (CH3OH) of the pendant groups link the chains together.

scholarly journals A Brief Review of Generalized Entropies

Entropy ◽  
2018 ◽  
Vol 20 (11) ◽  
pp. 813 ◽  
Author(s):  
José Amigó ◽  
Sámuel Balogh ◽  
Sergio Hernández
Keyword(s):  
Diffusion Processes ◽  
Complex Dynamics ◽  
Probability Distributions ◽  
Point Of View ◽  
Scaling Exponent ◽  
Scaling Exponents ◽  
Physical Systems ◽  
New Phenomena ◽  
Generalized Entropies

Entropy appears in many contexts (thermodynamics, statistical mechanics, information theory, measure-preserving dynamical systems, topological dynamics, etc.) as a measure of different properties (energy that cannot produce work, disorder, uncertainty, randomness, complexity, etc.). In this review, we focus on the so-called generalized entropies, which from a mathematical point of view are nonnegative functions defined on probability distributions that satisfy the first three Shannon–Khinchin axioms: continuity, maximality and expansibility. While these three axioms are expected to be satisfied by all macroscopic physical systems, the fourth axiom (separability or strong additivity) is in general violated by non-ergodic systems with long range forces, this having been the main reason for exploring weaker axiomatic settings. Currently, non-additive generalized entropies are being used also to study new phenomena in complex dynamics (multifractality), quantum systems (entanglement), soft sciences, and more. Besides going through the axiomatic framework, we review the characterization of generalized entropies via two scaling exponents introduced by Hanel and Thurner. In turn, the first of these exponents is related to the diffusion scaling exponent of diffusion processes, as we also discuss. Applications are addressed as the description of the main generalized entropies advances.

scholarly journals Solar wind low-frequency magnetohydrodynamic turbulence: extended self-similarity and scaling laws

1996 ◽  
Vol 3 (4) ◽  
pp. 247-261 ◽  
Author(s):  
V. Carbone ◽  
P. Veltri ◽  
R. Bruno
Keyword(s):  
Solar Wind ◽  
Scaling Laws ◽  
Velocity Structure ◽  
Fluid Flows ◽  
Structure Functions ◽  
Point Of View ◽  
Self Similarity ◽  
Extended Self ◽  
Scaling Exponents ◽  
Magnetohydrodynamic Turbulence

Abstract. In this paper we review some of the work done in investigating the scaling properties of Magnetohydrodynamic turbulence, by using velocity fluctuations measurements performed in the interplanetary space plasma by the Helios spacecraft. The set of scaling exponents ξq for the q-th order velocity structure functions, have been determined by using the Extended Self-Similarity hypothesis. We have found that the q-th order velocity structure function, when plotted vs. the 4-th order structure function, displays a range of self-similarity which extends over all the lengths covered by measurements, thus allowing for a very good determination of ξq. Moreover the results seem to show that the scaling exponents are the same regardless the various observation periods considered. The obtained scaling exponents have been compared with the results of some intermittency models for Kraichnan's turbulence, derived in the framework of infinitely divisible fragmentation processes, showing the good agreement between these models and our observations. Finally, on the basis of the actually available data sets, we show that scaling laws in Solar Wind turbulence seem to be different from turbulent scaling laws in the ordinary fluid flows. This is true for high-order velocity structure functions, while low-order velocity structure functions show the same scaling laws. Since our measurements involve length scales which extend over many order of magnitude where dissipation is practically absent, our results show that Solar Wind turbulence can be regarded as a testing bench for the investigation of general scaling behaviour in turbulent flows. In particular our results strongly support the point of view which attributes a key role to the inertial range dynamics in determining the intermittency characteristics in fluid flows, in contrast with the point of view which attributes intermittency to a finite Reynolds number effect.

Thermodynamics of Helix formation in small peptides of varying lengthin vacuo, implicit solvent and explicit solvent: Comparison between AMBER force fields

2019 ◽  
Vol 18 (03) ◽  
pp. 1950015
Author(s):  
Zhaoxi Sun ◽  
Xiaohui Wang
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Hydrogen Bonds ◽  
Force Fields ◽  
Implicit Solvent ◽  
Conformational Ensemble ◽  
Helix Formation ◽  
Solvent Models ◽  
Explicit Solvent ◽  
Amber Force Fields

Helix formation is of great significance in protein folding. The helix-forming tendencies of amino acids are accumulated along the sequence to determine the helix-forming tendency of peptides. Computer simulation can be used to model this process in atomic details and give structural insights. In the current work, we employ equilibrate-state free energy simulation to systematically study the folding/unfolding thermodynamics of a series of mutated peptides. Two AMBER force fields including AMBER99SB and AMBER14SB are compared. The new 14SB force field uses refitted torsion parameters compared with 99SB and they share the same atomic charge scheme. We find that in vacuo the helix formation is mutation dependent, which reflects the different helix propensities of different amino acids. In general, there are helix formers, helix indifferent groups and helix breakers. The helical structure becomes more favored when the length of the sequence becomes longer, which arises from the formation of additional backbone hydrogen bonds in the lengthened sequence. Therefore, the helix indifferent groups and helix breakers will become helix formers in long sequences. Also, protonation-dependent helix formation is observed for ionizable groups. In 14SB, the helical structures are more stable than in 99SB and differences can be observed in their grouping schemes, especially in the helix indifferent group. In solvents, all mutations are helix indifferent due to protein–solvent interactions. The decrease in the number of backbone hydrogen bonds is the same with the increase in the number of protein–water hydrogen bonds. The 14SB in explicit solvent is able to capture the free energy minima in the helical state while 14SB in implicit solvent, 99SB in explicit solvent and 99SB in implicit solvent cannot. The helix propensities calculated under 14SB agree with the corresponding experimental values, while the 99SB results obviously deviate from the references. Hence, implicit solvent models are unable to correctly describe the thermodynamics even for the simple helix formation in isolated peptides. Well-developed force fields and explicit solvents are needed to correctly describe the protein dynamics. Aside from the free energy, differences in conformational ensemble under different force fields in different solvent models are observed. The numbers of hydrogen bonds formed under different force fields agree and they are mostly determined by the solvent model.

scholarly journals The Metabolome and Osteoarthritis: Possible Contributions to Symptoms and Pathology

Metabolites ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 92 ◽  
Author(s):  
Jason Rockel ◽  
Mohit Kapoor
Keyword(s):  
Amino Acids ◽  
Synovial Fluid ◽  
Biological Sample ◽  
Response To Therapy ◽  
Patient Specific ◽  
Synovial Joint ◽  
Disease Pathogenesis ◽  
Potential Impact

Osteoarthritis (OA) is a progressive, deteriorative disease of articular joints. Although traditionally viewed as a local pathology, biomarker exploration has shown that systemic changes can be observed. These include changes to cytokines, microRNAs, and more recently, metabolites. The metabolome is the set of metabolites within a biological sample and includes circulating amino acids, lipids, and sugar moieties. Recent studies suggest that metabolites in the synovial fluid and blood could be used as biomarkers for OA incidence, prognosis, and response to therapy. However, based on clinical, demographic, and anthropometric factors, the local synovial joint and circulating metabolomes may be patient specific, with select subsets of metabolites contributing to OA disease. This review explores the contribution of the local and systemic metabolite changes to OA, and their potential impact on OA symptoms and disease pathogenesis.

The Contents of Macromolecule Solutes in Flexor Tendon Sheath Fluid and Their Relation to Synovial Fluid

1992 ◽  
Vol 17 (2) ◽  
pp. 167-171 ◽  
Author(s):  
L. HAGBERG ◽  
D. HEINEGÅRD ◽  
K. OHLSSON
Keyword(s):  
Synovial Fluid ◽  
Flexor Tendon ◽  
Adhesion Formation ◽  
Tendon Healing ◽  
Tendon Sheath ◽  
Point Of View ◽  
Joint Fluid ◽  
Molecular Weights ◽  
Sheath Fluid ◽  
Flexor Tendon Sheath

The importance of synovial environment for minimal adhesion formation in flexor tendon healing has recently gained attention. Various techniques have been used to restore an injured synovial tendon sheath. Therefore a quantitative analysis of flexor tendon sheath fluid is of interest to increase our knowledge about the specific synovial milieu and to evaluate the success of different types of sheath reconstructions from a biochemical point of view. Samples of tendon sheath fluid from trigger digits and tendon sheaths containing ganglions have been assayed for contents of hyaluronic acid and proteins of different molecular weights. The results show concentrations of hyaluronate and several proteins similar to those in normal joint fluid. These results indicate that flexor tendon sheath fluid has a character similar to synovial fluid of joints and apparently has specific functions such as soft tissue lubrication and nutrition of avascular tendon tissue.

Sign in / Sign up

Export Citation Format

Share Document