A Computational Protein Structure Refinement of the Yeast Acetohydroxyacid Synthase

Abstract

A combined molecular modeling and molecular dynamics simulation was carried out to obtain an improved description of the yeast acetohydroxyacid synthase (AHAS) in aqueous solution. After a thorough homology modeling, the AHAS catalytic dimer was subjected to a molecular dynamics (MD) simulation to analyze its behavior and optimize its geometry. The AHAS 3D molecular structure was analyzed according to the number of salt bridges and hydrogen bonds formed. During 20 ns of MD simulation, an average fluctuation of 3.9 Å was obtained. The cofactor thiamine diphosphate makes a relevant contribution to the system stability; this hypothesis was confirmed by the decrease in the average fluctuation of 0.3 Å. Moreover, the Ramachandran plot revealed no denaturation framework during the time of the simulation. ]]>

Antibody-mediated biorecognition of myelin oligodendrocyte glycoprotein: computational evidence of demyelination-related epitopes

“…As can be seen from Table 1, hydrogen bonds and salt bridges values are inversely proportional, which is in agreement with Franca et al . 27 and our previous work 28 results. This situation may be explained by two factors: (i) salt bridges are weakened by solvation effects 26 , and (ii) charged amino acids induce new hydrogen bonds with water molecules 27,28 .…”

“…27 and our previous work 28 results. This situation may be explained by two factors: (i) salt bridges are weakened by solvation effects 26 , and (ii) charged amino acids induce new hydrogen bonds with water molecules 27,28 . Thus, the number of salt bridges decreases and, consequently, the conformational fluctuation is induced along the simulation (Fig.…”

“…Salt bridges formation was monitored via VMD Salt Bridge plugin according to Ierich et al . 28 protocol. A salt bridge was quantified when the distance between the oxygen atom of an acidic residue and the nitrogen atom of a basic residue was shorter than 3.2 Å. Additionally, differences between the initial atomic coordinates and new positions assumed by residues during the simulation were measured using RMSD values.…”

Modelagem molecular voltada para a construção de um nanobiossensor para detecção do herbicida Imazaquin

“…A presença de densidade eletrônica altamente negativa nestes átomos afeta o número de ligações de hidrogênio influindo diretamente na estrutura obtida ao final da dinâmica e na orientação das moléculas de água ao seu redor, resultando em um número maior de ligações de hidrogênio. Ademais, a similaridade no número de ligações de hidrogênio estabelecidas por estes átomos e o solvente e do tempo de vida das mesmas, deve-se ao efeito de ressonância referente ao deslocamento de elétrons sob o grupo ODI-CBI-OCI.5.3 SIMULAÇÃO DA ENZIMA AHAS E DO SISTEMA AHAS-IQEstudos anteriores, feitos por Ierich e colaboradores demonstraram que a presença de todos cofatores conferem estabilidade estrutural à forma dimérica da enzima AHAS(IERICH et al, 2015). Por essa razão e considerando que a estabilidade estrutural da enzima é de fundamental importância para o desenvolvimento de um nanobiossensor preciso(DA SILVA et al, 2013, o sistema de partida foi a enzima AHAS na presença dos seus cofatores: FAD, TPP e Mg 2+ .…”