Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Summary

Protein design involves the construction of amino acid sequences and the incorporation of specific motifs to create functional variants. This approach is critical for the development of antimicrobial peptides (AMPs) to combat antibiotic-resistant pathogens. This paper presents a procedure for protein construction using various bioinformatics tools.

Abstract

The frontiers of protein design lie in the construction of amino acid sequences and the incorporation of specific motifs, such as binding sites, into receptors, ion channels, or other proteins. This approach allows the production of protein variants with specific functions and purposes. An exemplary application of these bioinformatics resources is the improvement of antimicrobial peptides (AMPs) or the design of synthetic AMPs. This development is significant because of the recent increase in emerging diseases, often caused by pathogens that are difficult to eradicate and exhibit antibiotic resistance. The consequences of this trend include the global extinction of animal species and human deaths. The rapid synthesis of novel and effective AMPs is, therefore, essential. These servers and programs can facilitate the rapid development of vaccines, AMPs, or effective treatments against these pathogens. The aim of this work was to present and propose a procedure for protein construction from sequences and to elucidate the process of using different tools to build these molecules step by step.

Introduction

The incidence of animal diseases is increasing, and this phenomenon is influenced by climate change. The rise in global temperature has led to the proliferation of microorganisms and the emergence of opportunistic pathogens, contributing to the development of virulent and drug-resistant diseases¹. Climate change affects the soil, water, skin, and gut microbiome, resulting in persistent stress on animal physiology and environmental adaptation. This phenomenon has been demonstrated to compromise immune responses, rendering animals more susceptible to emerging pathogens, which can have lethal consequences and potentially lead to the extinction of ....

Protocol

1. Identify molecular target sequences in Bd

NOTE: The selection of amino acids in the sequence is based on recommendations from the literature. Key amino acids include K, W, G, A, V, I, and L. To find out which programs to use, check the Table of Materials.

1. Retrieve target sequences from the NCBI database.
   1. Access the National Center for Biotechnology Information (NCBI) database at https://www.ncbi.nlm.nih.gov/.
   2. Select All Databases and choose Nucleotide as the search category.
   3. Enter <....

Results

The sequence under development utilizes the following formula: K(X)³KW(X)²K(X)²K, where (X) can be G, A, V, I, or L²⁸. The search results obtained included protein sequences of more than 300 amino acids, which were selected due to their status as complete protein sequences, as opposed to partial sequences. It should be noted that complete sequences are essential for the study. The functions of each receptor/membrane channel were also searched for within the sequenc.......

Discussion

The bioinformatics approach employed in protein structural prediction has inherent limitations due to its reliance on computational programs. These programs attempt to approximate real protein structures but are constrained by factors such as temperature, solubility, and solvent presence, which may not fully replicate in vivo conditions. Additionally, the method depends on the accurate identification of key conserved proteins through multiple alignments and curated databases, making the reliability of these databases cru.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
BLAST	N/A	N/A	Online server
Computer	AMD	N/A	SO: XP, W7, W8, W10, ubuntu, linux
HADDOCK server	BONVINLAB	N/A	Online server
HEX 5.2	BBSRC-INRIA	N/A	Download-Online server
I-TASSER	ZHANG LAB	N/A	Download-Online server
MUSCLE	N/A	N/A	Online server
NCBI	N/A	N/A	Online server
PYMOL	SCHRÖDINGER	N/A	Download-XP, W7, W8, W10, W11, LINUX
SWISS-MODEL	BIOZENTRUM	N/A	Online server
trRosetta server	YANG LAB	N/A	Online server
USCF CHIMERA	RBVI	N/A	Download-XP, W7, W8, W10, W11, LINUX