parameterization of modified amino acid residues into the thioredoxin protein structure

Lipid Türevleri ile Protein Karbonilasyonunun İn Silico Yapısal Analizi

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.

Yazar Spotlight: In Silico Oluşturma ve Karbonile Amino Asitlerin Protein Yapısı ve İşlevi Üzerindeki Etkisi

Moleküler Dinamik Simülasyonları Kullanılarak Yapısal Etkilerin Değerlendirilmesi için Reaktif Karbonillerle Modifiye Edilmiş Amino Asitlerin İnsiliko Sentezlenmesi 

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

Modifiye Amino Asit Kalıntılarının Tioredoksin Protein Yapısına Parametrelendirilmesi

Başlamak için, model protein sistemi olarak tioredoksin proteininin PDB dosyasını indirin. Protein yapısından su moleküllerini, dimerleri ve ligandları silmek için uygun bir protein görselleştirici yazılımı kullanın. Değiştirilmiş amino asit kalıntıları olan dosyayı lib'den ekleyin.PDB ve modifiye edilecek amino asit kalıntısı üzerine yerleştirin. from-lib'in amino ve karbonil uçlarının olduğundan emin olun. PDB, modifikasyon için amaçlanan amino asitle doğru bir şekilde eşleşir.Proteini silin, geriye sadece from-lib kalır. Değiştirilecek amino asit kalıntısının kapladığı üç boyutlu uzaydaki PDB dosyası. N ve C-terminal atomlarından hidrojeni çıkarın.from-lib'i kaydedin. PDB, U00 olarak taşındı. PDB'yi yeni koordinatlarla değiştirin.Bir metin düzenleyici kullanarak, temizlenmiş protein PDB dosyasını açın ve u00-moved. PDB dosyası. Koordinatları u00-moved konumundan kopyalayın.pdb ve modifiye edilmiş kalıntı ile protein sistemi arasındaki bağı uyarlamak için bunları protein PDB dosyasına yapıştırın. Tipolojiyi protein PDB formatıyla uyumlu olacak şekilde ayarlayın, HEATATM'yi ATOM olarak değiştirin ve bir rakamını değiştirilecek kalıntıya karşılık gelenle güncelleyin. Yeni dosyayı complex.pdb olarak kaydedin.AMBER'in moleküler dinamik simülasyonları ile karşılaştırıldığında m062x/631g seviyesindeki yoğunluk fonksiyonel teorisinden elde edilen yapılar, minimum bağ mesafesi hataları ve açı parametre değerleri göstererek teorik kuantum mekaniği ile iyi korelasyon gösterdi. Modifiye edilmiş amino asitlerin her biri için elde edilen RMSD değerleri, doğal muadillerine benzerdi ve tüm yörünge boyunca doğrulayıcı stabiliteyi korudu.

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 ...

Biyokimya

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

Lipid Peroksidasyon Aldehitleri ile Reaksiyona Giren Modifiye Amino Asitlerin Hesaplamalı Tasarımı ve Enerji Optimizasyonu