In the SARS-CoV-2 coronavirus, as in all viruses, structural flexibility and plasticity are of special relevance. The way in which SARS-CoV-2 infects our cells is explained by analyzing its molecular structure and, above all, by looking at the ductile regions of the proteins that form it.
The genetic material of viruses, in this case RNA, is packaged with thousands of small subunits of nucleoproteins inside a lipid envelope called a capsid that, in the case of coronaviruses, is shaped like a corona. The genome size of coronaviruses is larger than that of other RNA-type viruses. The SARS-CoV-2 genome encodes fourteen functional proteins.
Protein S (Spike – spike – in English), protein E (of the Envelope) and protein M (of the Membrane) are located in the capsid, which fulfill the structural function of assembling the virus and recognizing the cell Guest. Inside the capsid, there is the nucleoprotein N, which interacts with the viral RNA, providing it with stability. To these proteins are added another ten smaller structural ones and sixteen more non-structural ones that participate in the replication and transcription of the virus in the host cell.
The set of accessory and non-structural proteins has been called, somewhat literarily, the dark proteome of SARS-CoV-2. Although less studied, it contains important elements for the biology of the virus and its infectivity, as we will see shortly. Another characteristic to highlight of SARS-type viruses is that all their proteins have a tendency to bind to genetic material.
The structure of SARS-CoV-2
Since the pandemic began, the explosion of scientific work on SARS-CoV-2 has rapidly yielded numerous results on the structure of its proteins, many of them inspired by knowledge of other related viruses: SARS-CoV (known since 2002) and the MERS-CoV (known in 2012).
Since the middle of the 20th century, the study of the structure of proteins has been approached using biophysical techniques based on the interaction of electromagnetic radiation with matter, for example, spectroscopic techniques, which cover a range of possibilities as wide as that of the electromagnetic spectrum. But the success of studies with crystallography and X-ray diffraction has led to placing this technique in the first position of the ranking to solve the three-dimensional structure of these biomolecules at the atomic level and infer their function. Proof of this is that, to date, there are nearly four hundred SARS-CoV-2 structures resolved with this technique in 2020, according to data from the Protein Data Bank – the repository that records the known three-dimensional structures of proteins. and nucleic acids.
The structures resolved by other classical techniques, such as nuclear magnetic resonance (NMR) or neutron diffraction, are in the minority and do not reach ten. The extraordinary effort of the scientific community in this field during the last year is evident when we count that, in the period 2002-2019, the resolved structures of SARS-type viruses were close to half.
The SARS-CoV-2 protein S is by far the most studied by X-ray crystallography. There are up to one hundred and thirty-seven resolved three-dimensional structures. The extraordinary attention it has received is due to the fact that it is key to infection as it functions as the key to enter the virus into the host cell by attaching itself to the ACE2 receptor protein that acts as a lock in the oral mucosa, the main route of entry into body. It is, therefore, decisive in the fusion of the viral membrane with the host cell by allowing the release of the virus genome and causing infection.
Nucleoprotein N follows with thirteen structures resolved so far and participates in the intracellular process of replication and transcription of the virus genome.
The resolution of the structures of the ‘SARS-CoV-2 dark proteome’ is poor, in part due to the difficulty of finding homologous proteins available in other viruses or of resolving their ductile regions. As an alternative, microscopy techniques are contributing to the knowledge of their role, surely relevant, in the biology of the virus.
Ductile regions of proteins influence infectivity
Some structural elements of proteins escape the experimental procedures of crystallography and X-ray diffraction. But they are still important, on the contrary, they are often crucial for their functioning. That lack of structure is a useful feature.
Ductile regions (IDRs) are biologically active and highly dynamic in molecular recognition, in binding with other biomolecules or atoms (DNA, RNA, proteins, sugars, metals) and in the assembly of molecular complexes. They can rapidly adopt interconvertible conformations under different physiological conditions. Thus, structured and flexible elements complement each other.
Viral proteins contain a large number of ductile regions and various studies correlate this characteristic with virulence. In SARS-CoV-2, as in all viruses, ductile regions establish interactions with other proteins and with genetic material. For example, in the N nucleoprotein, its high proportion of flexible regions allows a close interaction with the viral RNA and with other membrane proteins, such as the M glycoprotein, which is the most abundant in the virus, or with the proteins of the virus. host cell, thus being multifunctional.
The rest of the SARS-CoV-2 proteins, including the S protein, have a moderate or low content of ductile regions, but some of them can be crucial to modulate the infection. In a recent work published in Nature, up to 332 interactions have been found between SARS-CoV-2 proteins and human proteins. Most of them feature protein S and the non-structural accessory proteins Nsp7 and Nsp8 of the virus. The flexibility and movement of the S proteins in the envelope of the capsid (they are counted up to about forty units) is decisive for the recognition of cell membranes and their binding to them. In several works, with the help of high-resolution electron cryomicroscopy, it has been proven that there is a continuous and characteristic flexibility in protein S, which is what makes this virus different from other coronaviruses.
As suggested, the ductile regions of the ‘SARS-CoV-2 dark proteome’ are also relevant. Computational and computer tools provide valuable information on whether or not a protein adopts a well-defined three-dimensional structure, and whether or not a flexible region is involved in molecular recognition. The recent study published in Cellular and Molecular Life Sciences concludes that almost all SARS-CoV-2 proteins have one or more molecular recognition segments. Increased flexibility in specific regions of proteins correlates with infectivity. In some cases, the predictions associated with these correlations become tested.
A recent work published in Nature shows clinical evidence that the D614G mutation in the SARS-CoV-2 protein S, detected in a variant that emerged in Europe during the month of January, increases replication in lung epithelial cells and in primary tissues of the respiratory tract, thereby enhancing infectivity. This mutation – a substitution of aspartate for glycine – implies a loss of complexity in the sequence and a gain in local flexibility. A strong phenotypic change related to virulence and associated with a glycine mutation has also been described in the bacterium Mycobacterium tuberculosis.
The relationship between ductility and infectivity is being useful in the design of new therapies aimed at blocking the entry of the virus into the cell or its replication. Some of the vaccine and antiviral drug designs attempt to block specific protein sites inspired by this knowledge to prevent infection. It is an open door to hope.
Inmaculada Yruela Guerrero, CSIC Scientific Researcher, Aula Dei Experimental Station (EEAD – CSIC)
This article was originally published on The Conversation. Read the original.
