Transmembrane Membrane Readers form a Novel Class of Proteins That Include Peripheral Phosphoinositide Recognition Domains and Viral Spikes

Overduin, Michael; Tran, Anh; Eekels, Dominic M.; Overduin, Finn; Kervin, Troy A.

doi:10.3390/membranes12111161

Cited by 4 publications

(1 citation statement)

References 149 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Another key influence during fusion, interacting with various portions of the protein, is the membrane. In fact, the TMD is believed to interact both with the viral envelope and the target membrane at some point during fusion, and a variety of mechanisms via which this could take place have been hypothesised (see [74] for more detail). Furthermore, not least due to their peculiar physicochemical properties, tryptophan residues have been shown to contribute to lipid ordering when positioned on the water/membrane interface [75].…”

Section: Beyond the Tmd Trimermentioning

confidence: 99%

Inconspicuous Yet Indispensable: The Coronavirus Spike Transmembrane Domain

Aliper,

Efremov

2023

IJMS

View full text Add to dashboard Cite

Membrane-spanning portions of proteins’ polypeptide chains are commonly known as their transmembrane domains (TMDs). The structural organisation and dynamic behaviour of TMDs from proteins of various families, be that receptors, ion channels, enzymes etc., have been under scrutiny on the part of the scientific community for the last few decades. The reason for such attention is that, apart from their obvious role as an “anchor” in ensuring the correct orientation of the protein’s extra-membrane domains (in most cases functionally important), TMDs often actively and directly contribute to the operation of “the protein machine”. They are capable of transmitting signals across the membrane, interacting with adjacent TMDs and membrane-proximal domains, as well as with various ligands, etc. Structural data on TMD arrangement are still fragmentary at best due to their complex molecular organisation as, most commonly, dynamic oligomers, as well as due to the challenges related to experimental studies thereof. Inter alia, this is especially true for viral fusion proteins, which have been the focus of numerous studies for quite some time, but have provoked unprecedented interest in view of the SARS-CoV-2 pandemic. However, despite numerous structure-centred studies of the spike (S) protein effectuating target cell entry in coronaviruses, structural data on the TMD as part of the entire spike protein are still incomplete, whereas this segment is known to be crucial to the spike’s fusogenic activity. Therefore, in attempting to bring together currently available data on the structure and dynamics of spike proteins’ TMDs, the present review aims to tackle a highly pertinent task and contribute to a better understanding of the molecular mechanisms underlying virus-mediated fusion, also offering a rationale for the design of novel efficacious methods for the treatment of infectious diseases caused by SARS-CoV-2 and related viruses.

show abstract

Section: Beyond the Tmd Trimermentioning

confidence: 99%

Inconspicuous Yet Indispensable: The Coronavirus Spike Transmembrane Domain

Aliper,

Efremov

2023

IJMS

View full text Add to dashboard Cite

show abstract

Comprehensive classification of proteins based on structures that engage lipids by COMPOSEL

Overduin

Kervin

Klarenbach

et al. 2023

Biophysical Chemistry

View full text Add to dashboard Cite

AlphaFold2 and its applications in the fields of biology and medicine

Yang

Zeng

Zhao

et al. 2023

Sig Transduct Target Ther

155

View full text Add to dashboard Cite

AlphaFold2 (AF2) is an artificial intelligence (AI) system developed by DeepMind that can predict three-dimensional (3D) structures of proteins from amino acid sequences with atomic-level accuracy. Protein structure prediction is one of the most challenging problems in computational biology and chemistry, and has puzzled scientists for 50 years. The advent of AF2 presents an unprecedented progress in protein structure prediction and has attracted much attention. Subsequent release of structures of more than 200 million proteins predicted by AF2 further aroused great enthusiasm in the science community, especially in the fields of biology and medicine. AF2 is thought to have a significant impact on structural biology and research areas that need protein structure information, such as drug discovery, protein design, prediction of protein function, et al. Though the time is not long since AF2 was developed, there are already quite a few application studies of AF2 in the fields of biology and medicine, with many of them having preliminarily proved the potential of AF2. To better understand AF2 and promote its applications, we will in this article summarize the principle and system architecture of AF2 as well as the recipe of its success, and particularly focus on reviewing its applications in the fields of biology and medicine. Limitations of current AF2 prediction will also be discussed.

show abstract

Transmembrane Membrane Readers form a Novel Class of Proteins That Include Peripheral Phosphoinositide Recognition Domains and Viral Spikes

Cited by 4 publications

References 149 publications

Inconspicuous Yet Indispensable: The Coronavirus Spike Transmembrane Domain

Inconspicuous Yet Indispensable: The Coronavirus Spike Transmembrane Domain

Comprehensive classification of proteins based on structures that engage lipids by COMPOSEL

AlphaFold2 and its applications in the fields of biology and medicine

Contact Info

Product

Resources

About