parameterization of modified amino acid residues into the thioredoxin protein structure

Analisi strutturale in silico della carbonilazione delle proteine da parte di derivati lipidici

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.

Autore in primo piano: Creazione in silico e impatto degli amminoacidi carbonilati sulla struttura e la funzione delle proteine

Sintesi di amminoacidi modificati con carbonili reattivi in silico per valutare gli effetti strutturali utilizzando simulazioni di dinamica molecolare 

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

Parametrizzazione dei residui di amminoacidi modificati nella struttura della proteina tioredossina

Per iniziare, scarica il file PDB della proteina tioredossina come sistema proteico modello. Utilizzare un software di visualizzazione delle proteine appropriato per cancellare le molecole d'acqua, i dimeri e i ligandi dalla struttura proteica. Aggiungere la lima con i residui di amminoacidi modificati da lib.PDB e sovrapporlo sul residuo amminoacidico da modificare. Assicurarsi che le estremità amminiche e carboniliche di from-lib. Il PDB corrisponde accuratamente all'amminoacido destinato alla modifica.Elimina la proteina, lasciando solo il from-lib. pdb nello spazio tridimensionale occupato dal residuo amminoacidico da modificare. Rimuovere l'idrogeno dagli atomi N e C-terminali.Salva il file from-lib. pdb come u00-spostato. pdb con le nuove coordinate.Utilizzando un editor di testo, apri il file PDB della proteina pulito e u00-moved. file pdb. Copia le coordinate da u00-moved.pdb e incollarli nel file PDB della proteina per adattare il legame tra il residuo modificato e il sistema proteico. Regolare la tipologia in modo che sia compatibile con il formato PDB della proteina, cambiando HEATATM in ATOM e aggiornando il numero uno a quello corrispondente al residuo da modificare. Salvare il nuovo file come complex.pdb.Le strutture della teoria del funzionale della densità a livello m062x/631g confrontate con le simulazioni di dinamica molecolare di AMBER si correlano bene con la meccanica quantistica teorica, mostrando errori minimi di distanza di legame e valori dei parametri angolari. I valori di RMSD ottenuti per ciascuno degli amminoacidi modificati erano simili alle controparti native e hanno mantenuto la stabilità di conferma durante l'intera traiettoria.

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 ...

Ricerca

Biochimica

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

Progettazione computazionale e ottimizzazione energetica di amminoacidi modificati che reagiscono con aldeidi di perossidazione lipidica