Predicting the stability of mutant proteins by computational approaches: an overview

2020 ◽  
Author(s):  
Anna Marabotti ◽  
Bernardina Scafuri ◽  
Angelo Facchiano
Keyword(s):  
Protein Engineering ◽  
Thermodynamic Stability ◽  
Genetic Diseases ◽  
Web Servers ◽  
Computational Approaches ◽  
Mutant Proteins ◽  
General Reliability ◽  
The Stability ◽  
The One ◽  
The Web

Abstract A very large number of computational methods to predict the change in thermodynamic stability of proteins due to mutations have been developed during the last 30 years, and many different web servers are currently available. Nevertheless, most of them suffer from severe drawbacks that decrease their general reliability and, consequently, their applicability to different goals such as protein engineering or the predictions of the effects of mutations in genetic diseases. In this review, we have summarized all the main approaches used to develop these tools, with a survey of the web servers currently available. Moreover, we have also reviewed the different assessments made during the years, in order to allow the reader to check directly the different performances of these tools, to select the one that best fits his/her needs, and to help naïve users in finding the best option for their needs.

Aromaticity in pericondensed cyclopenta-fused polycyclic aromatic hydrocarbons determined by density functional theory nucleus-independent chemical shifts and the Y-rule — Implications in oil asphaltene stability

2009 ◽  
Vol 87 (10) ◽  
pp. 1280-1295 ◽  
Author(s):  
Yosadara Ruiz-Morales
Keyword(s):  
Density Functional Theory ◽  
Thermodynamic Stability ◽  
Density Functional ◽  
Chemical Shifts ◽  
Functional Theory ◽  
Electronic Distribution ◽  
Polycyclic Aromatic ◽  
Minimum Number ◽  
The Stability ◽  
The One

The characterization of the stability of the fused aromatic region (FAR) in oil asphaltenes in terms of kinetic and thermodynamic stability is primary. Such an understanding is important if we are to get the optimal use from the heavy fraction of any crude oil. The FAR region is composed of pericondensed cyclopenta-fused polycyclic aromatic hydrocarbon compounds (CPPAHs) with N, S, and O heteroatoms. The Clar model, which states that the most important representation of a PAH is one having the maximum number of disjoint π-sextets, depicted by inscribed circles, and a minimum number of fixed double bonds, captures the essence of the kinetic and thermodynamic stability arguments. This model is readily employed for complex aromatics of the sort to be considered for asphaltenes. In the present research we prove that the aromaticity of CPPAHs can be assessed by using the qualitative easy-to-apply Y-rule. In the literature, it is proven that the Y-rule is applicable to elucidate the aromaticity of benzenoid PAHs and it has been validated for pericondensed benzenoid PAHs but not for pericondensed CPPAHs. Here, we verify that it is applicable for CPPAHs. The applicability of the Y-rule has been theoretically proven by comparing the π-electronic distribution obtained with it with the one obtained from nucleus-independent chemical shift (NICS) calculations at the density functional theory (DFT) level. The importance of doing this is that due to the polydispersity in the composition of the oil asphaltenes, and to understand their aromatic core structure, it is necessary to be able to asses the aromaticity of many cyclopenta-fused PAHs (possibly more than 500), of different sizes (up to 15 rings between hexagons and pentagons), and different spatial rearrangements in a quick but realistic and effective way. To try to do this with NICS will be very time consuming and computationally expensive, especially in the case of big systems.

scholarly journals A Python-WSGI and PHP-Apache Web Server Performance Analysis by Search Page Generator (SPG)

2021 ◽  
Vol 5 (1) ◽  
pp. 132-138
Author(s):  
Hataw Jalal Mohammed ◽  
Kamaran Hama Ali Faraj
Keyword(s):  
Computer Architecture ◽  
Source Code ◽  
Web Server ◽  
The Other ◽  
Web Database ◽  
Web Servers ◽  
Web Technologies ◽  
Server Side ◽  
The One ◽  
The Web

The web servers (WSGI-Python) and (PHP-Apache) are in middleware tier architecture. Middleware architecture is between frontend tier and backend tier, otherwise it’s a connection between frontend tier and backend tier for three tier architecture. The ELearning systems are designed by two different dynamic web technologies. First is by Python-WSGI and the second is by Personal Home Page (PHP-Apache). The two websites were designed with different open source and cross platform web technologies programming language namely; Python and PHP in the same structure and weight will evaluate perform over two different operating systems (OSs): 1) Windows-16 and 2) Linux-Ubuntu 20.4. Both systems run over the same computer architecture (64bit) as a server side with a common backend MySQL web database for both of them. Nevertheless, the middleware for PHP is a cross Apache MySQL PHP Perl (XAMPP), but the middleware for Python is Pycharm and the web server gateway interface (WSGI). WSGI and Apache are both web servers and this paper will show which of them has a better response time (RT). On the one hand, the experimental results demonstrate that the Python-WSGI is even weightier in Mbyte than PHP-Apache, on the other hand Python is still faster and more accurate than PHP. The designed SPG is by handwriting codes: one time designed the SPG by PHP source code and the other time designed by Python source code. Both Python-WSGI and PHP-Apache results are targeted to compare by the least time in milliseconds and take in to account enhanced performance.

Use of a Lyophilized Reference Plasma to Compare Coagulation Test Procedures

1975 ◽  
Vol 34 (02) ◽  
pp. 426-444 ◽  
Author(s):  
J Kahan ◽  
I Nohén
Keyword(s):  
Oral Anticoagulant Therapy ◽  
Repeated Measurements ◽  
Test Procedures ◽  
Coagulation Activity ◽  
Close Relationship ◽  
Measured Activity ◽  
Test Materials ◽  
The Difference ◽  
The Stability ◽  
The One

SummaryIn 4 collaborative trials, involving a varying number of hospital laboratories in the Stockholm area, the coagulation activity of different test materials was estimated with the one-stage prothrombin tests routinely used in the laboratories, viz. Normotest, Simplastin-A and Thrombotest. The test materials included different batches of a lyophilized reference plasma, deep-frozen specimens of diluted and undiluted normal plasmas, and fresh and deep-frozen specimens from patients on long-term oral anticoagulant therapy.Although a close relationship was found between different methods, Simplastin-A gave consistently lower values than Normotest, the difference being proportional to the estimated activity. The discrepancy was of about the same magnitude on all the test materials, and was probably due to a divergence between the manufacturers’ procedures used to set “normal percentage activity”, as well as to a varying ratio of measured activity to plasma concentration. The extent of discrepancy may vary with the batch-to-batch variation of thromboplastin reagents.The close agreement between results obtained on different test materials suggests that the investigated reference plasma could be used to calibrate the examined thromboplastin reagents, and to compare the degree of hypocoagulability estimated by the examined PIVKA-insensitive thromboplastin reagents.The assigned coagulation activity of different batches of the reference plasma agreed closely with experimentally obtained values. The stability of supplied batches was satisfactory as judged from the reproducibility of repeated measurements. The variability of test procedures was approximately the same on different test materials.

Structure, Stability and Water Adsorption on Ultra-Thin TiO2 Supported on TiN

2019 ◽  
Author(s):  
Jose Julio Gutierrez Moreno ◽  
Marco Fronzi ◽  
Pierre Lovera ◽  
alan O'Riordan ◽  
Mike J Ford ◽  
...  
Keyword(s):  
Density Functional ◽  
Water Adsorption ◽  
Chemical Potential ◽  
Energy Gap ◽  
Molecular Water ◽  
Structure Stability ◽  
Ambient Conditions ◽  
Rutile Structure ◽  
The Stability ◽  
The One

<p></p><p>Interfacial metal-oxide systems with ultrathin oxide layers are of high interest for their use in catalysis. In this study, we present a density functional theory (DFT) investigation of the structure of ultrathin rutile layers (one and two TiO<sub>2</sub> layers) supported on TiN and the stability of water on these interfacial structures. The rutile layers are stabilized on the TiN surface through the formation of interfacial Ti–O bonds. Charge transfer from the TiN substrate leads to the formation of reduced Ti<sup>3+</sup> cations in TiO<sub>2.</sub> The structure of the one-layer oxide slab is strongly distorted at the interface, while the thicker TiO<sub>2</sub> layer preserves the rutile structure. The energy cost for the formation of a single O vacancy in the one-layer oxide slab is only 0.5 eV with respect to the ideal interface. For the two-layer oxide slab, the introduction of several vacancies in an already non-stoichiometric system becomes progressively more favourable, which indicates the stability of the highly non-stoichiometric interfaces. Isolated water molecules dissociate when adsorbed at the TiO<sub>2</sub> layers. At higher coverages the preference is for molecular water adsorption. Our ab initio thermodynamics calculations show the fully water covered stoichiometric models as the most stable structure at typical ambient conditions. Interfacial models with multiple vacancies are most stable at low (reducing) oxygen chemical potential values. A water monolayer adsorbs dissociatively on the highly distorted 2-layer TiO<sub>1.75</sub>-TiN interface, where the Ti<sup>3+</sup> states lying above the top of the valence band contribute to a significant reduction of the energy gap compared to the stoichiometric TiO<sub>2</sub>-TiN model. Our results provide a guide for the design of novel interfacial systems containing ultrathin TiO<sub>2</sub> with potential application as photocatalytic water splitting devices.</p><p></p>

Thermodynamic Stability of Hexagonal and Rhombohedral Bn at Cvd Conditions from Van der Waals Corrected First Principles Calculations

2019 ◽  
Author(s):  
Henrik Pedersen ◽  
Björn Alling ◽  
Hans Högberg ◽  
Annop Ektarawong
Keyword(s):  
Thin Films ◽  
Thermodynamic Stability ◽  
First Principles ◽  
Thermal Equilibrium ◽  
Density Functional ◽  
Van Der Waals ◽  
Chemical Vapor ◽  
First Principles Calculations ◽  
Functional Theory ◽  
The Stability

Thin films of boron nitride (BN), particularly the sp<sup>2</sup>-hybridized polytypes hexagonal BN (h-BN) and rhombohedral BN (r-BN) are interesting for several electronic applications given band gaps in the UV. They are typically deposited close to thermal equilibrium by chemical vapor deposition (CVD) at temperatures and pressures in the regions 1400-1800 K and 1000-10000 Pa, respectively. In this letter, we use van der Waals corrected density functional theory and thermodynamic stability calculations to determine the stability of r-BN and compare it to that of h-BN as well as to cubic BN and wurtzitic BN. We find that r-BN is the stable sp<sup>2</sup>-hybridized phase at CVD conditions, while h-BN is metastable. Thus, our calculations suggest that thin films of h-BN must be deposited far from thermal equilibrium.

scholarly journals A Conceptual Model of Long-Term Weight Loss Maintenance: The Importance of Cognitive, Empirical and Computational Approaches

2021 ◽  
Vol 18 (2) ◽  
pp. 635
Author(s):  
Darren Haywood ◽  
Blake J. Lawrence ◽  
Frank D. Baughman ◽  
Barbara A. Mullan
Keyword(s):  
Weight Loss ◽  
Weight Loss Maintenance ◽  
Computational Approaches ◽  
Healthy Habits ◽  
Health Related ◽  
The One ◽  
Major Factors ◽  
Positive Social Support ◽  
Weight Loss Interventions

Living with obesity is related to numerous negative health outcomes, including various cancers, type II diabetes, and cardiovascular disease. Although much is known about the factors associated with obesity, and a range of weight loss interventions have been established, changing health-related behaviours to positively affect obesity outcomes has proven difficult. In this paper, we first draw together major factors that have emerged within the literature on weight loss to describe a new conceptual framework of long-term weight loss maintenance. Key to this framework is the suggestion that increased positive social support influences a reduction in psychosocial stress, and that this has the effect of promoting better executive functioning which in turn facilitates the development of healthy habits and the breaking of unhealthy habits, leading to improved ongoing maintenance of weight loss. We then outline how the use of computational approaches are an essential next step, to more rigorously test conceptual frameworks, such as the one we propose, and the benefits that a mixture of conceptual, empirical and computational approaches offer to the field of health psychology.

scholarly journals Stability of a one-dimensional morphoelastic model for post-burn contraction

2021 ◽  
Vol 83 (3) ◽  
Author(s):  
Ginger Egberts ◽  
Fred Vermolen ◽  
Paul van Zuijlen
Keyword(s):  
Wound Healing ◽  
Residual Stresses ◽  
Truncation Error ◽  
Signaling Molecules ◽  
Discrete Problem ◽  
One Dimensional ◽  
Stability Constraint ◽  
Biological Interpretation ◽  
The Stability ◽  
The One

AbstractTo deal with permanent deformations and residual stresses, we consider a morphoelastic model for the scar formation as the result of wound healing after a skin trauma. Next to the mechanical components such as strain and displacements, the model accounts for biological constituents such as the concentration of signaling molecules, the cellular densities of fibroblasts and myofibroblasts, and the density of collagen. Here we present stability constraints for the one-dimensional counterpart of this morphoelastic model, for both the continuous and (semi-) discrete problem. We show that the truncation error between these eigenvalues associated with the continuous and semi-discrete problem is of order $${{\mathcal {O}}}(h^2)$$ O ( h 2 ) . Next we perform numerical validation to these constraints and provide a biological interpretation of the (in)stability. For the mechanical part of the model, the results show the components reach equilibria in a (non) monotonic way, depending on the value of the viscosity. The results show that the parameters of the chemical part of the model need to meet the stability constraint, depending on the decay rate of the signaling molecules, to avoid unrealistic results.

scholarly journals Investigation of the Stability of Yeast rad52 Mutant Proteins Uncovers Post-translational and Transcriptional Regulation of Rad52p

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 91-101 ◽  
Author(s):  
Erin N Asleson ◽  
Dennis M Livingston
Keyword(s):  
Half Life ◽  
Translational Regulation ◽  
Cellular Level ◽  
Missense Mutations ◽  
Wild Type ◽  
Mutant Proteins ◽  
Gal1 Promoter ◽  
Rad52 Protein ◽  
The Stability ◽  
Mutant Forms

Abstract We investigated the stability of the Saccharomyces cerevisiae Rad52 protein to learn how a cell controls its quantity and longevity. We measured the cellular levels of wild-type and mutant forms of Rad52p when expressed from the RAD52 promoter and the half-lives of the various forms of Rad52p when expressed from the GAL1 promoter. The wild-type protein has a half-life of 15 min. rad52 mutations variably affect the cellular levels of the protein products, and these levels correlate with the measured half-lives. While missense mutations in the N terminus of the protein drastically reduce the cellular levels of the mutant proteins, two mutations—one a deletion of amino acids 210-327 and the other a missense mutation of residue 235—increase the cellular level and half-life more than twofold. These results suggest that Rad52p is subject to post-translational regulation. Proteasomal mutations have no effect on Rad52p half-life but increase the amount of RAD52 message. In contrast to Rad52p, the half-life of Rad51p is &gt;2 hr, and RAD51 expression is unaffected by proteasomal mutations. These differences between Rad52p and Rad51p suggest differential regulation of two proteins that interact in recombinational repair.

scholarly journals Prediction of Functional Consequences of Missense Mutations in ANO4 Gene

2021 ◽  
Vol 22 (5) ◽  
pp. 2732
Author(s):  
Nadine Reichhart ◽  
Vladimir M. Milenkovic ◽  
Christian H. Wetzel ◽  
Olaf Strauß
Keyword(s):  
Transmembrane Protein ◽  
Functional Characterization ◽  
Missense Mutations ◽  
Mutant Proteins ◽  
Functional Consequences ◽  
New Perspective ◽  
The Stability ◽  
Dynamics Simulations ◽  
And Function

The anoctamin (TMEM16) family of transmembrane protein consists of ten members in vertebrates, which act as Ca2+-dependent ion channels and/or Ca2+-dependent scramblases. ANO4 which is primarily expressed in the CNS and certain endocrine glands, has been associated with various neuronal disorders. Therefore, we focused our study on prioritizing missense mutations that are assumed to alter the structure and stability of ANO4 protein. We employed a wide array of evolution and structure based in silico prediction methods to identify potentially deleterious missense mutations in the ANO4 gene. Identified pathogenic mutations were then mapped to the modeled human ANO4 structure and the effects of missense mutations were studied on the atomic level using molecular dynamics simulations. Our data show that the G80A and A500T mutations significantly alter the stability of the mutant proteins, thus providing new perspective on the role of missense mutations in ANO4 gene. Results obtained in this study may help to identify disease associated mutations which affect ANO4 protein structure and function and might facilitate future functional characterization of ANO4.

scholarly journals One-Dimensional Organic–Inorganic Material (C6H9N2)2BiCl5: From Synthesis to Structural, Spectroscopic, and Electronic Characterizations

2021 ◽  
Vol 22 (4) ◽  
pp. 2030
Author(s):  
Hela Ferjani ◽  
Hammouda Chebbi ◽  
Mohammed Fettouhi
Keyword(s):  
Hydrogen Bonding ◽  
Density Functional ◽  
Crystal Packing ◽  
Diffuse Reflectance Spectrum ◽  
Enrichment Ratio ◽  
One Dimensional ◽  
Organic Part ◽  
Fukui Indices ◽  
The Stability ◽  
The One

The new organic–inorganic compound (C6H9N2)2BiCl5 (I) has been grown by the solvent evaporation method. The one-dimensional (1D) structure of the allylimidazolium chlorobismuthate (I) has been determined by single crystal X-ray diffraction. It crystallizes in the centrosymmetric space group C2/c and consists of 1-allylimidazolium cations and (1D) chains of the anion BiCl52−, built up of corner-sharing [BiCl63−] octahedra which are interconnected by means of hydrogen bonding contacts N/C–H⋯Cl. The intermolecular interactions were quantified using Hirshfeld surface analysis and the enrichment ratio established that the most important role in the stability of the crystal structure was provided by hydrogen bonding and H···H interactions. The highest value of E was calculated for the contact N⋯C (6.87) followed by C⋯C (2.85) and Bi⋯Cl (2.43). These contacts were favored and made the main contribution to the crystal packing. The vibrational modes were identified and assigned by infrared and Raman spectroscopy. The optical band gap (Eg = 3.26 eV) was calculated from the diffuse reflectance spectrum and showed that we can consider the material as a semiconductor. The density functional theory (DFT) has been used to determine the calculated gap, which was about 3.73 eV, and to explain the electronic structure of the title compound, its optical properties, and the stability of the organic part by the calculation of HOMO and LUMO energy and the Fukui indices.

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