NMR Methods for Studying Protein–Protein Interactions Involved in Translation Initiation

Background: NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems. Objective: This review provides a toolkit to investigate peptide conformational properties by NMR. Methods: Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through Pubmed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well. Results: The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well. Conclusion: NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.

Download Full-text

NMR Spectroscopy of supramolecular chemistry on protein surfaces

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.16.203 ◽

2020 ◽

Vol 16 ◽

pp. 2505-2522

Author(s):

Peter Bayer ◽

Anja Matena ◽

Christine Beuck

Keyword(s):

Nmr Spectroscopy ◽

Supramolecular Chemistry ◽

Molecular Interactions ◽

Protein Interactions ◽

Atomic Resolution ◽

Protein Protein Interactions ◽

Protein Surfaces ◽

Interaction Partners ◽

Binding Pockets ◽

Nmr Methods

As one of the few analytical methods that offer atomic resolution, NMR spectroscopy is a valuable tool to study the interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to modulate protein–protein interactions. Here we present NMR methods that have been applied to characterize these molecular interactions and discuss the challenges of this endeavor.

Download Full-text

Molecular Structure and Functional Elucidation of IF-3 Protein of Chloroflexus Aurantiacus Involved in Protein Biosynthesis: An In-Silico Approach

10.26434/chemrxiv.14342372.v1 ◽

2021 ◽

Author(s):

Abu Saim Mohammad Saikat

Keyword(s):

Translation Initiation ◽

Protein Interactions ◽

In Silico ◽

Tertiary Structure ◽

Protein Biosynthesis ◽

Translation Initiation Factor ◽

Initiation Factor ◽

Chloroflexus Aurantiacus ◽

Protein Protein Interactions ◽

Functional Interpretation

Chloroflexus aurantiacus is a thermophilic bacterium that produces a multitude of proteins within its genome. Bioinformatics strategies can facilitate comprehending this organism through functional and structural interpretation assessments. This study aimed to allocate the structure and function through an in-silico approach required for bacterial protein biosynthesis. This in-silico viewpoint provides copious properties, including the physicochemical properties, subcellular location, three-dimensional structure, protein-protein interactions, and functional elucidation of the protein (WP_012256288.1). The STRING program is utilized for the explication of protein-protein interactions. The in-silico investigation documented the protein's hydrophilic nature with predominantly alpha (α) helices in its secondary structure. The tertiary-structure model of the protein has been shown to exhibit reasonably high consistency based on various quality assessment methods. The functional interpretation suggested that the protein can act as a translation initiation factor, a protein required for translation and protein biosynthesis. Protein-protein interactions also demonstrated high credence that the protein interconnected with 30S ribosomal subunit involved in protein synthesis. This study is bioinformatically examined that the protein (WP_012256288.1) is affiliated in protein biosynthesis as a translation initiation factor IF-3 of C. aurantiacus.

Download Full-text

Structural and Functional Elucidation of IF-3 Protein of Chloroflexus aurantiacus Involved in Protein Biosynthesis: An In-Silico Approach

10.26434/chemrxiv.14342372.v2 ◽

2021 ◽

Author(s):

Abu Saim Mohammad Saikat ◽

Md. Ekhlas Uddin ◽

Tasnim Ahmad ◽

Shahriar Mahmud ◽

Md. Abu Sayeed Imran ◽

...

Keyword(s):

Translation Initiation ◽

Protein Interactions ◽

In Silico ◽

Tertiary Structure ◽

Protein Biosynthesis ◽

Translation Initiation Factor ◽

Initiation Factor ◽

Chloroflexus Aurantiacus ◽

Protein Protein Interactions ◽

Functional Interpretation

Chloroflexus aurantiacus is a thermophilic bacterium that produces a multitude of proteins within its genome. Bioinformatics strategies can facilitate comprehending this organism through functional and structural interpretation assessments.This study aimed to allocate the structure and function through an in-silico approach required for bacterial protein biosynthesis. This in-silico viewpoint provides copious properties, including the physicochemical properties, subcellular location, three-dimensional structure, protein-protein interactions, and functional elucidation of the protein (WP_012256288.1). The STRING program is utilized for the explication of protein-protein interactions. The in-silico investigation documented the protein's hydrophilic nature with predominantly alpha (α) helices in its secondary structure.The tertiary-structure model of the protein has been shown to exhibit reasonably high consistency based on various quality assessment methods.The functional interpretation suggested that the protein can act as a translation initiation factor, a protein required for translation and protein biosynthesis. Protein-protein interactions also demonstrated high credence that the protein interconnected with 30S ribosomal subunit involved in protein synthesis. This study is bioinformatically examined that the protein (WP_012256288.1) is affiliated in protein biosynthesis as a translation initiation factor IF-3 of C. aurantiacus.

Download Full-text

NMR Methods for Exploring ‘Dark’ States in Ligand Binding and Protein-Protein Interactions

Progress in Nuclear Magnetic Resonance Spectroscopy ◽

10.1016/j.pnmrs.2021.10.001 ◽

2021 ◽

Author(s):

Vitali Tugarinov ◽

Alberto Ceccon ◽

G. Marius Clore

Keyword(s):

Ligand Binding ◽

Protein Interactions ◽

Protein Protein Interactions ◽

Nmr Methods

Download Full-text

RING fingers and B-boxes: zinc-binding protein-protein interaction domains

Biochemistry and Cell Biology ◽

10.1139/o98-021 ◽

1998 ◽

Vol 76 (2-3) ◽

pp. 351-358 ◽

Cited By ~ 140

Author(s):

Katherine LB Borden

Keyword(s):

Conformational Changes ◽

Protein Interaction ◽

Protein Interactions ◽

Structural Features ◽

Zinc Binding ◽

Protein Protein Interactions ◽

Protein Protein Interaction ◽

Biological Studies ◽

Interaction Domains ◽

Nmr Methods

The cysteine-rich zinc-binding motifs known as the RING and B-box are found in several unrelated proteins. Structural, biochemical, and biological studies of these motifs reveal that they mediate protein-protein interactions. Several RING-containing proteins are oncoproteins and recent data indicate that proapoptotic activities can be mediated through the RING. 1H NMR methods were used to determine the structures of RINGs and a B-box domain and to monitor the conformational changes these motifs undergo upon zinc ligation. This review discusses in detail the structural features of the RING and B-box domains. Further, possible structure function relationships for these motifs particularly in their role as protein interaction domains are discussed.Key words: RING, B-box, PML, NMR.

Download Full-text

Molecular Structure and Functional Elucidation of IF-3 Protein of Chloroflexus Aurantiacus Involved in Protein Biosynthesis: An In-Silico Approach

10.26434/chemrxiv.14342372 ◽

2021 ◽

Author(s):

Abu Saim Mohammad Saikat

Keyword(s):

Translation Initiation ◽

Protein Interactions ◽

In Silico ◽

Tertiary Structure ◽

Protein Biosynthesis ◽

Translation Initiation Factor ◽

Initiation Factor ◽

Chloroflexus Aurantiacus ◽

Protein Protein Interactions ◽

Functional Interpretation

Chloroflexus aurantiacus is a thermophilic bacterium that produces a multitude of proteins within its genome. Bioinformatics strategies can facilitate comprehending this organism through functional and structural interpretation assessments. This study aimed to allocate the structure and function through an in-silico approach required for bacterial protein biosynthesis. This in-silico viewpoint provides copious properties, including the physicochemical properties, subcellular location, three-dimensional structure, protein-protein interactions, and functional elucidation of the protein (WP_012256288.1). The STRING program is utilized for the explication of protein-protein interactions. The in-silico investigation documented the protein's hydrophilic nature with predominantly alpha (α) helices in its secondary structure. The tertiary-structure model of the protein has been shown to exhibit reasonably high consistency based on various quality assessment methods. The functional interpretation suggested that the protein can act as a translation initiation factor, a protein required for translation and protein biosynthesis. Protein-protein interactions also demonstrated high credence that the protein interconnected with 30S ribosomal subunit involved in protein synthesis. This study is bioinformatically examined that the protein (WP_012256288.1) is affiliated in protein biosynthesis as a translation initiation factor IF-3 of C. aurantiacus.

Download Full-text

Structural and Functional Elucidation of IF-3 Protein of Chloroflexus aurantiacus Involved in Protein Biosynthesis: An In Silico Approach

BioMed Research International ◽

10.1155/2021/9050026 ◽

2021 ◽

Vol 2021 ◽

pp. 1-10

Author(s):

Abu Saim Mohammad Saikat ◽

Md. Ekhlas Uddin ◽

Tasnim Ahmad ◽

Shahriar Mahmud ◽

Md. Abu Sayeed Imran ◽

...

Keyword(s):

Translation Initiation ◽

Protein Interactions ◽

In Silico ◽

Tertiary Structure ◽

Protein Biosynthesis ◽

Translation Initiation Factor ◽

Initiation Factor ◽

Chloroflexus Aurantiacus ◽

Protein Protein Interactions ◽

Functional Interpretation

Chloroflexus aurantiacus is a thermophilic bacterium that produces a multitude of proteins within its genome. Bioinformatics strategies can facilitate comprehending this organism through functional and structural interpretation assessments. This study is aimed at allocating the structure and function through an in silico approach required for bacterial protein biosynthesis. This in silico viewpoint provides copious properties, including the physicochemical properties, subcellular location, three-dimensional structure, protein-protein interactions, and functional elucidation of the protein (WP_012256288.1). The STRING program is utilized for the explication of protein-protein interactions. The in silico investigation documented the protein’s hydrophilic nature with predominantly alpha (α) helices in its secondary structure. The tertiary-structure model of the protein has been shown to exhibit reasonably high consistency based on various quality assessment methods. The functional interpretation suggested that the protein can act as a translation initiation factor, a protein required for translation and protein biosynthesis. Protein-protein interactions also demonstrated high credence that the protein interconnected with 30S ribosomal subunit involved in protein synthesis. This study bioinformatically examined that the protein (WP_012256288.1) is affiliated in protein biosynthesis as a translation initiation factor IF-3 of C. aurantiacus.

Download Full-text