Reply to "Identification of thermodynamic quantities of the stability of peptide-MHC I complex using nanoscale differential scanning fluorimetry" by Jakob Harris and Jonghoon Kang

2022 ◽  
Vol 141 ◽  
pp. 257
Author(s):  
Sebastian Springer
2016 ◽  
Vol 94 (10) ◽  
pp. 1045-1053 ◽  
Author(s):  
Ahmad Sheykhi ◽  
Seyed Hossein Hendi ◽  
Fatemeh Naeimipour ◽  
Shahram Panahiyan ◽  
Behzad Eslam Panah

It was shown that with the combination of three Liouville-type dilaton potentials, one can derive dilaton black holes in the background of anti-de-Sitter (AdS) spaces. In this paper, we further extend the study on the dilaton AdS black holes by investigating their thermodynamic instability through a geometry approach. First, we review thermodynamic quantities of the solutions and check the validity of the first law of thermodynamics. Then, we investigate phase transitions and stability of the solutions. In particular, we disclose the effects of the dilaton field on the stability of the black holes. We also employ the geometrical approach toward thermodynamical behavior of the system and find that the divergencies in the Ricci scalar coincide with roots and divergencies in the heat capacity. We find that the behavior of the Ricci scalar around divergence points depends on the type of the phase transition.


2016 ◽  
Vol 6 (1) ◽  
pp. 26
Author(s):  
Jennifer Turner Waldo ◽  
Tsering Dolma ◽  
Emily Rouse

<p class="1Body">The heterodecameric Dam1 complex is involved in establishing and maintaining the connection between the kinetochore and the mitotic spindle during mitosis. Biochemical studies of the reconstituted complex have shed light upon how it interacts with microtubules. However, little information about the biochemical properties of the isolated subunits has been available. This report examines the stability and structure of Dad2p, one of the Dam1 complex subunits isolated from <em>Candida albicans</em>. By employing differential scanning fluorimetry, protease protection and hydrodynamic analyses, we show that Dad2p is specifically responsive to the presence of divalent cations. This observation may be important for understanding the dynamic structure and regulation of the Dam1 complex in fungal cells.</p>


2015 ◽  
Vol 71 (10) ◽  
pp. 1359-1364 ◽  
Author(s):  
Marko Ristic ◽  
Nicholas Rosa ◽  
Shane A. Seabrook ◽  
Janet Newman

There is strong evidence to suggest that a protein sample needs to be well folded and uniform in order to form protein crystals, and it is accepted knowledge that the formulation can have profound effects on the behaviour of the protein sample. The technique of differential scanning fluorimetry (DSF) is a very accessible method to determine protein stability as a function of the formulation chemistry and the temperature. A diverse set of 252 soluble protein samples was subjected to a standard formulation-screening protocol using DSF. Automated analysis of the DSF results suggest that in over 35% of cases buffer screening significantly increases the stability of the protein sample. Of the 28 standard formulations tested, three stood out as being statistically better than the others: these included a formulation containing the buffer citrate, long known to be `protein friendly'; bis-tris and ADA were also identified as being very useful buffers in protein formulations.


2021 ◽  
Vol 81 (12) ◽  
Author(s):  
Seyed Hossein Hendi ◽  
Somayeh Hajkhalili ◽  
Mubasher Jamil ◽  
Mehrab Momennia

AbstractIn this paper, we investigate the thermodynamics and phase transitions of a four-dimensional rotating Kaluza–Klein black hole solution in the presence of Maxwell electrodynamics. Calculating the conserved and thermodynamic quantities shows that the first law of thermodynamics is satisfied. To find the stable black hole’s criteria, we check the stability in the canonical ensemble by analyzing the behavior of the heat capacity. We also consider a massive scalar perturbation minimally coupled to the background geometry of the four-dimensional static Kaluza–Klein black hole and investigate the quasinormal modes by employing the Wentzel–Kramers–Brillouin (WKB) approximation. The anomalous decay rate of the quasinormal modes spectrum is investigated by using the sixth-order WKB formula and quasi-resonance modes of the black hole are studied with averaging of Padé approximations as well.


Biology ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1197
Author(s):  
Éva Bulyáki ◽  
Judit Kun ◽  
Tamás Molnár ◽  
Alexandra Papp ◽  
András Micsonai ◽  
...  

β2-microglobulin (β2m), the light chain of the MHC-I complex, is associated with dialysis-related amyloidosis (DRA). Recently, a hereditary systemic amyloidosis was discovered, caused by a naturally occurring D76N β2m variant, which showed a structure remarkably similar to the wild-type (WT) protein, albeit with decreased thermodynamic stability and increased amyloidogenicity. Here, we investigated the role of the D76N mutation in the amyloid formation of β2m by point mutations affecting the Asp76-Lys41 ion-pair of WT β2m and the charge cluster on Asp38. Using a variety of biophysical techniques, we investigated the conformational stability and partial unfolding of the native state of the variants, as well as their amyloidogenic propensity and the stability of amyloid fibrils under various conditions. Furthermore, we studied the intermolecular interactions of WT and mutant proteins with various binding partners that might have in vivo relevance. We found that, relative to WT β2m, the exceptional amyloidogenicity of the pathogenic D76N β2m variant is realized by the deleterious synergy of diverse effects of destabilized native structure, higher sensitivity to negatively charged amphiphilic molecules (e.g., lipids) and polyphosphate, more effective fibril nucleation, higher conformational stability of fibrils, and elevated affinity for extracellular components, including extracellular matrix proteins.


Entropy ◽  
2021 ◽  
Vol 23 (3) ◽  
pp. 358
Author(s):  
Gamal G. L. Nashed ◽  
Kazuharu Bamba

We explore the quadratic form of the f(R)=R+bR2 gravitational theory to derive rotating N-dimensions black hole solutions with ai,i≥1 rotation parameters. Here, R is the Ricci scalar and b is the dimensional parameter. We assumed that the N-dimensional spacetime is static and it has flat horizons with a zero curvature boundary. We investigated the physics of black holes by calculating the relations of physical quantities such as the horizon radius and mass. We also demonstrate that, in the four-dimensional case, the higher-order curvature does not contribute to the black hole, i.e., black hole does not depend on the dimensional parameter b, whereas, in the case of N>4, it depends on parameter b, owing to the contribution of the correction R2 term. We analyze the conserved quantities, energy, and angular-momentum, of black hole solutions by applying the relocalization method. Additionally, we calculate the thermodynamic quantities, such as temperature and entropy, and examine the stability of black hole solutions locally and show that they have thermodynamic stability. Moreover, the calculations of entropy put a constraint on the parameter b to be b<116Λ to obtain a positive entropy.


2016 ◽  
Author(s):  
Fabrizio Pucci ◽  
Raphaël Bourgeas ◽  
Marianne Rooman

We have set up and manually curated a dataset containing experimental information on the impact of amino acid substitutions in a protein on its thermal stability. It consists of a repository of experimentally measured melting temperatures (Tm) and their changes upon point mutations (∆Tm) for proteins having a well-resolved X-ray structure. This high-quality dataset is designed for being used for the training or benchmarking of in silico thermal stability prediction methods. It also reports other experimentally measured thermodynamic quantities when available,i.e.the folding enthalpy (∆H) and heat capacity (∆CP) of the wild type proteins and their changes upon mutations (∆∆H and ∆∆CP), as well as the change in folding free energy (∆∆G) at a reference temperature. These data are analyzed in view of improving our insights into the correlation between thermal and thermodynamic stabilities, the asymmetry between the number of stabilizing and destabilizing mutations, and the difference in stabilization potential of thermostable versus mesostable proteins.


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