scholarly journals An Integrated Structural and Computational Study of the Thermostability of Two Thioredoxin Mutants from Alicyclobacillus acidocaldarius

2003 ◽  
Vol 185 (14) ◽  
pp. 4285-4289 ◽  
Author(s):  
Simonetta Bartolucci ◽  
Giuseppina De Simone ◽  
Stefania Galdiero ◽  
Roberto Improta ◽  
Valeria Menchise ◽  
...  
Keyword(s):  
Amino Acids ◽  
Computational Analysis ◽  
Computational Study ◽  
Electrostatic Energy ◽  
Alicyclobacillus Acidocaldarius ◽  
Mutant Forms

ABSTRACT We report a crystallographic and computational analysis of two mutant forms of the Alicyclobacillus acidocaldarius thioredoxin (BacTrx) done in order to evaluate the contribution of two specific amino acids to the thermostability of BacTrx. Our results suggest that the thermostability of BacTrx may be modulated by mutations affecting the overall electrostatic energy of the protein.

Three-dimensional computational study in a corrugated pipe inserted system filled with phase change material

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Ömer Akbal ◽  
Hakan F. Öztop ◽  
Nidal H. Abu-Hamdeh
Keyword(s):  
Phase Change ◽  
Phase Change Material ◽  
Computational Analysis ◽  
Computational Study ◽  
Three Dimensional ◽  
Simple Algorithm ◽  
Melting Time ◽  
Geometrical Parameters ◽  
Content Type ◽  
Change Material

Purpose The purpose of this paper is to make a three-dimensional computational analysis of melting in corrugated pipe inserted system filled with phase change material (PCM). The system was heated from the inner pipe, and temperature of the outer pipe was lower than that of inner pipe. Different geometrical ratio cases and two different temperature differences were tested for their effect on melting time. Design/methodology/approach A computational analysis through a pipe with corrugated pipe filled with PCM is analyzed. Finite volume method was applied with the SIMPLE algorithm method to solve the governing equations. Findings The results indicate that the geometrical parameters can be used to control the melting time inside the heat exchanger which, in turn, affect the energy efficiency. The fastest melting time is seen in Case 4 at the same temperature difference which is the major observation of the current work. Originality/value Originality of this work is to perform a three-dimensional analysis of melting of PCM in a corrugated pipe inserted pipe.

A Computational Study on Airfoils at a Low Reynolds Number

2000 ◽  
Author(s):  
Ajit Pal Singh ◽  
S. H. Winoto ◽  
D. A. Shah ◽  
K. G. Lim ◽  
Robert E. K. Goh
Keyword(s):  
Reynolds Number ◽  
Computational Analysis ◽  
Computational Study ◽  
Low Reynolds Number ◽  
Micro Air Vehicles ◽  
Reynolds Numbers ◽  
Aerodynamic Performance ◽  
Low Reynolds Numbers ◽  
Study Results ◽  
Low Reynolds

Abstract Performance characteristics of some low Reynolds number airfoils for the use in micro air vehicles (MAVs) are computationally studied using XFOIL at a Reynolds number of 80,000. XFOIL, which is based on linear-vorticity stream function panel method coupled with a viscous integral formulation, is used for the analysis. In the first part of the study, results obtained from the XFOIL have been compared with available experimental data at low Reynolds numbers. XFOIL is then used to study relative aerodynamic performance of nine different airfoils. The computational analysis has shown that the S1223 airfoil has a relatively better performance than other airfoils considered for the analysis.

Computational Analysis of Non-Premixed Combustion in a Scramjet Combustor With a Wedge Shaped Strut Injector

2021 ◽  
Author(s):  
Sajal Katare ◽  
Nagendra P. Yadav
Keyword(s):  
Computational Analysis ◽  
Static Pressure ◽  
Computational Study ◽  
Combustion Process ◽  
Combustion Efficiency ◽  
Reaction Model ◽  
Premixed Combustion ◽  
Cold Flow ◽  
Flame Holder ◽  
Scramjet Combustor

Abstract This paper focuses the computational study of non-premixed combustion in a scramjet combustor. The wedge shaped strut injector was used in the combustion process. In order to investigate the flame holding mechanism of the wedge shaped strut in supersonic flow, the two-dimensional coupled implicit RANS equations, the standard k-ε turbulence model and the finite-rate/eddy-dissipation reaction model are introduced to simulate the flow field of the hydrogen fueled scramjet combustor with a strut flame holder under different conditions. The static pressure of the case under the engine ignition condition is much higher than that of the case under the cold flow condition. The reflection of shock waves improves the mixing of hydrogen with the stream of inlet air and thus increases combustion efficiency. The mass flow rate of air is optimized for the best performance of engine.

On the interaction between the imidazolium cation and aromatic amino acids. A computational study

2015 ◽  
Vol 13 (29) ◽  
pp. 7961-7972 ◽  
Author(s):  
Ana A. Rodríguez-Sanz ◽  
Enrique M. Cabaleiro-Lago ◽  
Jesús Rodríguez-Otero
Keyword(s):  
Amino Acids ◽  
Computational Study ◽  
Aromatic Amino Acids ◽  
Imidazolium Cation ◽  
Π Interactions

Phe, Tyr and Trp form parallel complexes with cation⋯π interactions. His complexes are the strongest, but without making contact with the aromatic cloud.

The unfolding effects on the protein hydration shell and partial molar volume: a computational study

2016 ◽  
Vol 18 (40) ◽  
pp. 28175-28182 ◽  
Author(s):  
Sara Del Galdo ◽  
Andrea Amadei
Keyword(s):  
Aqueous Solution ◽  
Computational Analysis ◽  
Computational Study ◽  
Hydration Shell ◽  
Partial Molar Volumes ◽  
Globular Proteins ◽  
Protein Hydration ◽  
Native Protein ◽  
Unfolded State ◽  
Protein Hydration Shell

In this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes.

scholarly journals Altering the solubility of the antibiotic candidate Nisin – a computational study

2020 ◽  
Author(s):  
Preeti Pandey ◽  
Ulrich H.E. Hansmann ◽  
Feng Wang
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Antimicrobial Activity ◽  
Broad Spectrum ◽  
Bacterial Resistance ◽  
Force Fields ◽  
Computational Study ◽  
Food Preservative ◽  
Drug Candidates ◽  
Dynamics Simulations

AbstractThe growing bacterial resistance to available antibiotics makes it necessary to look for new drug candidates. An example is a lanthionine-containing nisin, which has a broad spectrum of antimicrobial activity. While nisin is widely utilized as a food preservative, its poor solubility and low stability at physiological pH hinder its use as an antibiotic. As the solubility of nisin is controlled by the residues of the hinge region, we have performed molecular dynamics simulations of various mutants and studied their effects on nisin’s solubility. These simulations are complicated by the presence of two uncommon residues (dehydroalanine and dehydrobutyrine) in the peptide. The primary goal of the present study is to derive rules for designing new mutants that will be more soluble at physiological pH and, therefore, may serve as a basis for the future antibiotic design. Another aim of our study is to evaluate whether existing force fields can model the solubility of these amino acids accurately, in order to motivate further developments of force fields to account for solubility information.

scholarly journals Design of Potential SARS-CoV-2 Inhibitor

2020 ◽  
Vol 5 (9) ◽  
pp. 1043-1048
Author(s):  
F. J. Amaku ◽  
I. E. Otuokere ◽  
K. K. Igwe ◽  
O. V. Ikpeazu
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
Drug Interaction ◽  
Virtual Screening ◽  
Computational Study ◽  
Enzymatic Reaction ◽  
Target Protein ◽  
Web Servers ◽  
Zinc Database ◽  
Online Web

This computational study comprises of pharmacophore-base virtual screening of the ZINC database, molecular docking of predicted ligands (pharmacophore agent) against the target protein, SARS-CoV-2 (PDB ID: 5r7y) and the prediction of ADMET descriptors using Swiss ADME and PROTOX-II online web servers.  Meanwhile,  remdesivir, ZINC72392503, ZINC72809903, ZINC06560017, ZINC76101700, ZINC88423098 and ZINC91600695 had a docking scores of -2.0 Kcal/mol, -6.7 Kcal/mol, -6.4 Kcal/mol, -6.0 Kcal/mol, -6.0 Kcal/mol, -6.0 Kcal/mol and-6.0 Kcal/mol respectively.  Meanwhile, ZINC72392503 was selected as the lead molecule and was observed to interact with LUE 27, THR 25, CYS 145, THR 26, SER 46, GLY 143, ASN 142, HIS 163, HIS 41, MET 165, GLU 166, ARG 188, GLN 189, HIS 41, MET 49, SER 46 amino acids.  The ADME descriptor revealed that the lead molecule was soluble, druggable, void of drug-drug interaction that may inhibit essential enzymatic reaction and was noticed to fall into PROTOX-II toxicity class 3.  The lead molecule showed a good affinity for the target protein of SARS-CoV-2, hence, may have a physiological implication that can inhibit a protein responsible for the replication of SARS-CoV-2.

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