parameterization of modified amino acid residues into the thioredoxin protein structure

Analyse structurale in silico de la carbonylation des protéines par des dérivés lipidiques

In the constant pursuit of understanding the molecular behavior of proteins with oxidative modifications, computational chemistry has become a fundamental pillar in the broad field of scientific research. This relies on the use of theoretical models capable of interpreting physical phenomena in electronic systems, using mathematical equations to describe the atomic behavior of molecules. Within this landscape, computational simulations of proteins stand out as crucial tools to analyze the atomic behavior of molecular systems. Based on the evaluation of structural behavior, energetic calculations, and conformational states1, these methods become strategic allies to predict the behavior of biomolecular systems.
These simulations specialize in studying structural changes and assessing the loss or gain of biological functions in protein systems. However, computational approaches have shown significant limitations when applied to protein systems containing modified residues formed by covalent post-translational modifications in the sequence. This is because many available methods lack resources with parameters adaptable to force fields that are compatible with the most common packages of programs for molecular dynamics simulations of proteins2,3,4,5,6. Therefore, the standardization of computational software-compatible force-field adaptive parameters is essential to facilitate the precise coupling of topologies and atomic coordinates with the equation governing the potential energy of the system7.
In response to these challenges, a protocol adaptable to new modified amino acid residues with aldehydes derived from lipid peroxidation has been developed using ab initio methods. In that sense, the optimization of the structural geometry of the new residues allows the assignment of adaptive charges to new bond, angle, and dihedral parameters that can be run in general force fields such as AMBER. Subsequent validation of these parameters allows the determination of the consistency and robustness of the method applicable to molecular dynamics simulations.
One of the notable strengths of this method lies in its ability to adapt to diverse post-translational modifications, from carbonylation to phosphorylation, acetylation, and methylation, among others. This versatility is not only limited to protein systems but extends to macromolecular structures, allowing coupling with atomic topologies and coordinates. In contrast, previous studies reveal that the standard parameterization of post-translational modifications is only suited to a specific type of modification and can only be obtained from published repositories, lacking the ability to create new structures8.
Currently, challenges in protein structure prediction and design are becoming more evident when modeling structures with post-translational modifications. The scarcity of parameters describing alterations at specific amino acid sites underlines the urgent need to develop and apply computational methods that can be adjusted to standard parameterizations. The aim of this protocol is to provide a route for the in silico construction of new parameters for amino acids covalently modified with reactive carbonyl species derived from fatty acid oxidation. These modified amino acids are recognized by the general amber force field (GAFF) and can, therefore, be used to evaluate in silico the structural and functional effects that this kind of carbonylation has on their target proteins.

Pleins feux sur l’auteur : Création in silico et impact des acides aminés carbonylés sur la structure et la fonction des protéines

Synthèse d’acides aminés modifiés avec des carbonyles réactifs in silico pour évaluer les effets structurels à l’aide de simulations de dynamique moléculaire 

Our work shows a route for the in silico creation of carbonylated amino acids with lipid peroxidation end products and on how to incorporate them into a protein. This can help us understand how this post-translational modification can alter the structural function of carbonylated proteins. Programs based on artificial intelligence algorithms are the most powerful computational tools today for predicting the tertiary structure of protein.However, they do not yet recognize carbonylated amino acids and therefore, they cannot predict their effects on protein structure. To study the impact of post-translational modification on the structure and function of a protein, a wide range of the parameter methods are available that are combined with computational approaches to accelerate and deepen the desired finding. There are important challenges that must be faced in the study of post-translational modification of proteins, both in vivo, in vitro, and in silico.At the in silico level, the improvement of force fields and data analysis programs is still required, along with the creation of new parameters. Due to the increase in carbonylated proteins in metabolic infections and aging-related diseases, among many others, our results can contribute to understanding the structural change that occur in this and how this can affect the function in silico

Paramétrisation de résidus d’acides aminés modifiés dans la structure de la protéine thiorédoxine

Pour commencer, téléchargez le fichier PDB de la protéine thiorédoxine en tant que système protéique modèle. Utilisez un logiciel de visualisation de protéines approprié pour effacer les molécules d’eau, les dimères et les ligands de la structure de la protéine. Ajoutez le fichier avec les résidus d’acides aminés modifiés from-lib.PDB et de le superposer sur le résidu d’acide aminé à modifier. Assurez-vous que les extrémités amino et carbonyle de from-lib. La PDB correspond exactement à l’acide aminé destiné à la modification.Supprimez la protéine, ne laissant que la from-lib. pdb dans l’espace tridimensionnel occupé par le résidu d’acide aminé à modifier. Retirez l’hydrogène des atomes N-terminaux et C-terminals.Enregistrez la bibliothèque from. PDB en tant que U00-déplacé. pdb avec les nouvelles coordonnées.À l’aide d’un éditeur de texte, ouvrez le fichier PDB de protéine nettoyé et déplacez-vous. fichier pdb. Copiez les coordonnées de u00-moved.PDB et collez-les dans le fichier PDB de la protéine pour adapter la liaison entre le résidu modifié et le système protéique. Ajustez la typologie pour qu’elle soit compatible avec le format PDB des protéines, en changeant HEATATM en ATOM et en mettant à jour le numéro un à celui correspondant au résidu à modifier. Enregistrez le nouveau fichier sous complex.pdb.Les structures de la théorie de la fonctionnelle de la densité au niveau m062x/631g comparées aux simulations de dynamique moléculaire d’AMBER étaient bien corrélées avec la mécanique quantique théorique, montrant des erreurs minimales de distance de liaison et des valeurs de paramètres d’angle. Les valeurs RMSD obtenues pour chacun des acides aminés modifiés étaient similaires à celles de leurs homologues natifs et ont maintenu la stabilité de confirmation tout au long de la trajectoire.

Research

JoVE Journal

Biochemistry

Parameterization of Modified Amino Acid Residues into the Thioredoxin Protein Structure

In Silico Structural Analysis of Protein Carbonylation by Lipid Derivatives

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations 

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Protein carbonylation by reactive aldehydes derived from lipid peroxidation leads to cross-linking, oligomerization, and aggregation of proteins, causing ...

Recherche

Biochimie

Computational Design and Energy Optimization of Modified Amino Acids Reacting with Lipid Peroxidation Aldehydes

Conception computationnelle et optimisation énergétique d’acides aminés modifiés réagissant avec des aldéhydes de peroxydation lipidique