Faculty Opinions recommendation of In silico relationship between configurational entropy and soft degrees of freedom in proteins and peptides.

2009 ◽  
Author(s):  
Dimitrios Morikis
Keyword(s):  
In Silico ◽  
Degrees Of Freedom ◽  
Configurational Entropy ◽  
Proteins And Peptides

scholarly journals Identification of Low Molecular Weight Proteins and Peptides from Schistosoma mekongi Worm, Egg and Infected Mouse Sera

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 559
Author(s):  
Tipparat Thiangtrongjit ◽  
Nattapon Simanon ◽  
Poom Adisakwattana ◽  
Yanin Limpanont ◽  
Phiraphol Chusongsang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Infected Mouse ◽  
In Silico ◽  
Limited Information ◽  
Schistosoma Mekongi ◽  
River Region ◽  
Precursor Proteins ◽  
Peptide Profiles ◽  
Low Sensitivity ◽  
Proteins And Peptides

Schistosoma mekongi is found in the lower Mekong river region and causes schistosomiasis. Low sensitivity of diagnosis and development of drug resistance are problems to eliminate this disease. To develop novel therapies and diagnostics for S. mekongi, the basic molecular biology of this pathogen needs to be explored. Bioactive peptides have been reported in several worms and play important roles in biological functions. Limited information is available on the S. mekongi peptidome. Therefore, this study aimed to identify S. mekongi peptides using in silico transcriptome mining and mass spectrometry approaches. Schistosoma peptide components were identified in adult worms, eggs, and infected mouse sera. Thirteen neuropeptide families were identified using in silico predictions from in-house transcriptomic databases of adult S. mekongi worms. Using mass spectrometry approaches, 118 peptides (from 54 precursor proteins) and 194 peptides (from 86 precursor proteins) were identified from adult worms and eggs, respectively. Importantly, eight unique peptides of the S. mekongi ubiquitin thioesterase, trabid, were identified in infected mouse sera 14, 28, and 56 days after infection. This protein may be a potential target for diagnosis of schistosomiasis. The S. mekongi peptide profiles determined in this study could be used for further drug and diagnostic development.

Cobaltites as perspective thermoelectrics

2005 ◽  
Vol 886 ◽  
Author(s):  
Jiri Hejtmánek ◽  
Miroslav Veverka ◽  
Karel Knižek ◽  
Hiroyuki Fujishiro ◽  
Sylvie Hebert ◽  
...  
Keyword(s):  
Degrees Of Freedom ◽  
Phonon Scattering ◽  
Configurational Entropy ◽  
Energy Difference ◽  
Charge Carriers ◽  
Material Research ◽  
Cobalt Ions ◽  
Similar Materials ◽  
Physical Background ◽  
Open Question

AbstractThe recent material research of mixed cobalt oxides is strongly motivated by the potential of some of them to be used as chemically stable high temperature thermoelectric material. This fact together with both the theoretical and experimental ambitions to fulfill the severe criteria needed for efficient thermoelectric conversion intensified both their theoretical and experimental research. Nonetheless, despite the investigations of the prototype materials represented by 3D perovskites Ln1−xAxCoO3 (Ln = La, Y, rare-earth, A = alkaline-earth) and 2D cobaltites of NaxCoO2 type, the concise physical background of their transport and magnetic properties remain still a matter of debate. This is likely due to a fact that cobalt ions can be stabilized either in low-spin state (diamagnetic for “pure” Co3+), with filled t2g levels and empty eg states, or magnetic ones, with filled eg states. As the energy difference between respective states is due to comparable strength of crystal field and Hund's energies rather small, the thermodynamically most stable ground-state, with eventually different character of charge carriers, can be critically influenced by an interplay of additional degrees of freedom - orbital and charge. The challenge for unequivocal theoretical model represents the thermoelectric power of mixed cobaltites where, up to now, somewhat ambiguous models based either on “classical” approach, associated with diffusion of itinerant charge carriers, or more exotic - based on configurational entropy of quasi-itinerant carriers - are often used for similar materials. Simultaneously, the open question remains the assessment of the dominant mechanism of phonon scattering in 2D cobaltites.

scholarly journals Exact Solution to the Extended Zwanzig Model for Quasi-Sigmoidal Chemically Induced Denaturation Profiles: Specific Heat and Configurational Entropy

2014 ◽  
Vol 2014 ◽  
pp. 1-11
Author(s):  
G. E. Aguilar-Pineda ◽  
L. Olivares-Quiroz
Keyword(s):  
Exact Solution ◽  
Analytical Solution ◽  
Specific Heat ◽  
Configurational Entropy ◽  
Naturally Occurring ◽  
Thermodynamic Potentials ◽  
Chemically Induced ◽  
Denaturation Profile ◽  
Average Internal Energy ◽  
Proteins And Peptides

Temperature and chemically induced denaturation comprise two of the most characteristic mechanisms to achieve the passage from the native state N to any of the unstructured states Dj in the denatured ensemble in proteins and peptides. In this work we present a full analytical solution for the configurational partition function 𝒵qs of a homopolymer chain poly-X in the extended Zwanzig model (EZM) for a quasisigmoidal denaturation profile. This solution is built up from an EZM exact solution in the case where the fraction α of native contacts follows exact linear dependence on denaturant’s concentration ζ; thus an analytical solution for 𝒵L in the case of an exact linear denaturation profile is also provided. A recently established connection between the number ν of potential nonnative conformations per residue and temperature-independent helical propensity ω complements the model in order to identify specific proteinogenic poly-X chains, where X represents any of the twenty naturally occurring aminoacid residues. From 𝒵qs, equilibrium thermodynamic potentials like entropy 𝒮 and average internal energy 〈E〉 and thermodynamic susceptibilities like specific heat C𝓋 are calculated for poly-valine (poly-V) and poly-alanine (poly-A) chains. The influence of the rate at which native contacts denature as function of ζ on thermodynamic stability is also discussed.

Oxides and the high entropy regime: A new mix for engineering physical properties

MRS Advances ◽  
2020 ◽  
Vol 5 (64) ◽  
pp. 3419-3436 ◽  
Author(s):  
P. B. Meisenheimer ◽  
J. T. Heron
Keyword(s):  
Physical Properties ◽  
Degrees Of Freedom ◽  
Equilibrium Phase ◽  
Configurational Entropy ◽  
Oxide Materials ◽  
Spin Orbital ◽  
Metal Insulator ◽  
High Entropy ◽  
Thin Film Epitaxy

AbstractHistorically, the enthalpy is the criterion for oxide materials discovery and design. In this regime, highly controlled thin film epitaxy can be leveraged to manifest bulk and interfacial phases that are non-existent in bulk equilibrium phase diagrams. With the recent discovery of entropy-stabilized oxides, entropy and disorder engineering has been realized as an orthogonal approach. This has led to the nucleation and rapid growth of research on high-entropy oxides – multicomponent oxides where the configurational entropy is large but its contribution to its stabilization need not be significant or is currently unknown. From current research, it is clear that entropy enhances the chemical solubility of species and can realize new stereochemical configurations which has led to the rapid discovery of new phases and compositions. The research has expanded beyond studies to understand the role of entropy in stabilization and realization of new crystal structures to now include physical properties and the roles of local and global disorder. Here, key observations made regarding the dielectric and magnetic properties are reviewed. These materials have recently been observed to display concerted symmetry breaking, metal-insulator transitions, and magnetism, paving the way for engineering of these and potentially other functional phenomena. Excitingly, the disorder in these oxides allows for new interplay between spin, orbital, charge, and lattice degrees of freedom to design the physical behavior. We also provide a perspective on the state of the field and prospects for entropic oxide materials in applications considering their unique characteristics.

scholarly journals Configurational entropy measurements in extremely supercooled liquids that break the glass ceiling

2017 ◽  
Vol 114 (43) ◽  
pp. 11356-11361 ◽  
Author(s):  
Ludovic Berthier ◽  
Patrick Charbonneau ◽  
Daniele Coslovich ◽  
Andrea Ninarello ◽  
Misaki Ozawa ◽  
...  
Keyword(s):  
Glass Transition ◽  
Glass Ceiling ◽  
In Silico ◽  
Configurational Entropy ◽  
Supercooled Liquids ◽  
Numerical Results ◽  
Computational Tools ◽  
Experimental Glass ◽  
Glass State ◽  
Numerical Studies

Liquids relax extremely slowly on approaching the glass state. One explanation is that an entropy crisis, because of the rarefaction of available states, makes it increasingly arduous to reach equilibrium in that regime. Validating this scenario is challenging, because experiments offer limited resolution, while numerical studies lag more than eight orders of magnitude behind experimentally relevant timescales. In this work, we not only close the colossal gap between experiments and simulations but manage to create in silico configurations that have no experimental analog yet. Deploying a range of computational tools, we obtain four estimates of their configurational entropy. These measurements consistently confirm that the steep entropy decrease observed in experiments is also found in simulations, even beyond the experimental glass transition. Our numerical results thus extend the observational window into the physics of glasses and reinforce the relevance of an entropy crisis for understanding their formation.

scholarly journals In Silico Analysis of Honeybee Venom Protein Interaction with Wild Type and Mutant (A82V + P375S) Ebola Virus Spike Protein

Biologics ◽  
2022 ◽  
Vol 2 (1) ◽  
pp. 45-55
Author(s):  
Muhammad Muzammal ◽  
Muzammil Ahmad Khan ◽  
Mohammed Al Mohaini ◽  
Abdulkhaliq J. Alsalman ◽  
Maitham A. Al Hawaj ◽  
...  
Keyword(s):  
Phospholipase A2 ◽  
Strong Interaction ◽  
In Silico ◽  
Ebola Virus ◽  
In Silico Analysis ◽  
Spike Protein ◽  
Honeybee Venom ◽  
Silico Analysis ◽  
Venom Proteins ◽  
Proteins And Peptides

Venom from different organisms was used in ancient times to treat a wide range of diseases, and to combat a variety of enveloped and non-enveloped viruses. The aim of this in silico research was to investigate the impact of honeybee venom proteins and peptides against Ebola virus. In the current in silico study, different online and offline tools were used. RaptorX (protein 3D modeling) and PatchDock (protein–protein docking) were used as online tools, while Chimera and LigPlot + v2.1 were used for visualizing protein–protein interactions. We screened nine venom proteins and peptides against the normal Ebola virus spike protein and found that melittin, MCD and phospholipase A2 showed a strong interaction. We then screened these peptides and proteins against mutated strains of Ebola virus and found that the enzyme phospholipase A2 showed a strong interaction. According to the findings, phospholipase A2 found in honeybee venom may be an effective source of antiviral therapy against the deadly Ebola virus. Although the antiviral potency of phospholipase A2 has been recorded previously, this is the first in silico analysis of honeybee phospholipase A2 against the Ebola viral spike protein and its more lethal mutant strain.

Structure solution of the basic decagonal Al–Co–Ni phase by the atomic surfaces modelling method

2001 ◽  
Vol 58 (1) ◽  
pp. 8-33 ◽  
Author(s):  
Antonio Cervellino ◽  
Torsten Haibach ◽  
Walter Steurer
Keyword(s):  
Degrees Of Freedom ◽  
Configurational Entropy ◽  
Spatial Arrangement ◽  
Structural Disorder ◽  
Range Interaction ◽  
Cell Parameters ◽  
Decagonal Phase ◽  
Structure Solution ◽  
The Stability ◽  
High Degree

The atomic surfaces modelling technique has been used to solve the structure of the basic Ni-rich Al–Co–Ni decagonal phase. Formula Al70.6Co6.7Ni22.7, space group P\overline{10}, five-dimensional unit-cell parameters: d 1 = d 4 = 4.752 (3) Å, d 2 = d 3 = 3.360 (2) Å, d 5 = 8.1710 (2) Å; α12 = α34 = 69.295°, α13 = α24 = 45°, α14 = 41.410°, α23 = α i5 = 90° (i = 1–4), V = 291.2 (7) Å5; Dx = 3.887 Mg m−3. Refinement based on |F|; 2767 unique reflections (|F| > 0), 749 parameters, R = 0.17, wR = 0.06. Describing the structure of quasicrystals embedded in n-dimensional superspace in principle takes advantage of n-dimensional periodicity to select the minimal set of degrees of freedom for the structure. The method of modelling of the atomic surfaces yielded the first fully detailed structure solution of this phase. Comparison with numerous former, less accurate models confirms several features already derived, but adds a new essential insight of the structure and its complexity. The atoms fill the space forming recurrent structure motifs, which we will (generically) refer to as clusters. However, no unique cluster exists, although differences are small. Each cluster shows a high degree of structural disorder. This gives rise to a large configurational entropy, as much as expected in a phase which is stable at high temperature. On the other side, the cluster spatial arrangement is perfectly quasiperiodic. These considerations, corroborated by analysis of the structural relationship with neighbouring periodic phases, strongly suggest the existence of a non-local, long-range interaction term in the total energy which may be essential to the stability.

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