Read Section 3 to 3.5 and answer the ff:-What biomolecule contains the genetic information of SARS-CoV-2? Be specific.-Describe the structure of the SARS-CoV-2.-What are the four main structural proteins in SARS-CoV-2? Briefly explain what each protein does.-How does SARS-CoV-2 bind to the host cell? Provide some evidences to support your answer.-What proteins can be targeted for therapeutic purposes (i.e. vaccines or antiviral drugs)? G. Galer, H. Özdemir, D. Omar et alinformation, Coronaviruses have infectious, non-segmented and asingle positive-sense RNA molecule. Coronaviruses and Torovirusesare within the virus family, Coronavidiae. While coronaviruses havepathogenic capacity on both animals and humans, Toroviruses areone of the main reasons for animal diarrhea (Peiris, 2012), Coro-naviruses can be divided into 4 groups known as alpha, beta, gammaand delta, and people commonly get infected by alpha and betacoronaviruses as known as: 229 E, NL63, OC43, and HKU1 (CDC.2020). They are well known for their positive single-strandedRNA genomes of approximately 30 kb, enveloped with nucleo-capsid (Perlman and Netland, 2009). Recent studies have alsoshown that current coronavirus threatening public health belongsto betacoronavirus (Huang et al., 2020). It is really important tounderstand the nature of a virus to come up with the right treat-ment, thus, the studies regarding its pathogenesis carry a valid role.To find a relation between SARS-CoV-2 and other coronaviruses, astudy calculated the sequence identity by collecting samples fromdifferent types. It was revealed that samples from COVID-19infected patients presented a close relationship with two bat-derived coronaviruses: bat-SL-COVZC45 and bat-SL-CoVZXC21. Infact, SARS-CoV-2 showed 88% identity with the two bat-derivedcoronaviruses. In comparison to these viruses, the associationsbetween SARS-CoV-2 and SARS-CoV as well as MERS-CoV weremore distant. While SARS-CoV showed -79% identity with SARS-CoV-2, MERS-CoV showed only -50% identity with SARS-CoV-2(Lu et al., 2020). It was also reported that SARS-CoV-2 is 96%identical at the whole-genome level to another bat coronavirus.(BatCoV-RaTG13) (Zhou et al., 2020). This close relationship mayprovide an evidence for SARS-CoV-2 to be originated in bats.With the spread of the virus, new variants and mutations havestarted to become a problem in some regions. In 2020 December, anew variant appeared in the UK; it was revealed that this newvariant was associated with the spike protein of the virus. In lateDecember, it caused increased number of cases in the southeast ofEngland. Authorities stated that the new mutation would not causea major problem within the vaccine, as the vaccine affects manyregions in the spike protein (Wise, 2020). A matched cohort studyrevealed the mortality rate to be slightly higher in the new strain(Challen et al., 2021). Another variant named 501Y.V2 was found inSouth Africa on December 18, 2020. It was discovered that this newvariant had spread to various provinces. Furthermore, this variantwas found to have 3 mutations in the spike protein (Tang et al.,ang et2021: "WHO | SARS-CoV-2 Variants," n. d.). Although the researchis still ongoing, according to a study, South African strain may bemore transmissible (Tegally et al., 2020),Coronavirus has one of the best studied genome structures sofar, and exhibits a high mutation rate (Cui et al, 2019). Mutations inthis novel virus significantly affected the chain of transmission.Although SARS-CoV-2 contains amino acid mutations in itsreceptor-binding domain (Lu et al., 2020), both SARS-CoV andSARS-CoV-2 use their spike proteins to recognize the angiotensinconverting enzyme 2 (ACE2) as a functional receptor on the targetcell for entry (Hoffmann et al., 2020; Lan et al., 2020; Letko et al..2020; Shang et al., 2020; Walls et al., 2020; Wang et al., 2020b;Yan et al., 2020). Recently, biophysical, and biochemical propertiesof SARS-CoV-2 have been studied in detail, which will be addressedin the following Sections 3 and 4.3. Structural and functional features of SARS-CoV-2Phylogenetic analyses revealed that SARS-CoV-2 belongs to thebetacoronavirus category of the Coronaviridae family. The corona-virus disease 2019 (COVID-19), rapidly spreading worldwide, iscaused by this novel RNA virus SARS-CoV-2. To fight this globalcrisis, effective treatment and vaccine alternatives against COVID-Progress in Biophysics and Molecular Biology 164 (2021) 3-1819 are urgently required. Obviously, understanding the structuraland functional features, dynamics and receptor recognitionmechanism of SARS-CoV-2 is the first crucial step to develop theeffective antiviral drug agents, novel targeted treatments, smallmolecular inhibitors, blocking antibodies, other therapeutics aswell as to design an effective preventive vaccine against COVID-19.Knowing the structures and interactions on the atomic level willguide to identify potential targets by applying, for instance, in silicostructure-assisted drug design or molecular docking procedures tofind new drugs or to repurpose already approved drugs (Estrada,2020; Hoffmann et al., 2020; Jin et al., 2020b). Hence, so farstructural and functional relationship of SARS-CoV-2 proteins havebeen extensively studied by using biophysical techniques (e.g.cryogenic electron microscopy (Cryo-EM), X-ray crystallography),along with biochemical and biological assays (Lan et al., 2020;Shang et al., 2020; Walls et al., 2020; Wang et al., 2020b; Wrappet al., 2020; Yan et al., 2020). Further studies on SARS-CoV-2 arestill ongoing with increasing tendency to have integrated knowl-edge about molecular basis of recognition, molecular and atomicinteractions as well as conformational changes occurring duringviral attachment and entering into human cells.Recently, biophysical and biochemical techniques have beenapplied for characterization of SARS-CoV-2 in the COVID-19 studies.Importantly, Cryo-EM (using deflection of electrons from frozenprotein samples at liquid nitrogen temperatures) and X-ray crys-tallography (using scattering of X-rays from well-ordered proteincrystals) have been used to determine the 3D structure of SARS-CoV-2 proteins at atomic resolution in a few Angstrom (A) range.Later on, the atomic coordinates and maps of the protein 3Dstructures have been deposited in the Protein Data Bank (PDB),freely available to global community. In this regard, Lan et al.determined the crystal structure of the receptor-binding domain(RBD) of SARS-CoV-2 spike protein bound to the cell receptor ACE2at 2.45 A resolution (PDB ID: 6M0J) by using X-ray diffraction data(Lan et al., 2020). They also identified the amino acid residues of theSARS-CoV-2 RBD, essential for the ACE2 binding. Walls et al.determined the cryo-EM structures of the SARS-CoV-2 S ectodo-main trimer in the closed (2.8 A resolution, PDB ID: 6VXX) andpartially opened (3.2 A resolution, PDB ID: 6VYB) conformations(Walls et al., 2020). In another work, Wrapp et al. determined thecryo-EM structure of the SARS-CoV-2 spike protein in the prefusionconformation at 3.46 A resolution and identified that one of thethree receptor-binding domains is 'up' in a receptor-accessibleconformation (PDB ID: 6VSB) (Wrapp et al., 2020). They alsoshowed that SARS-CoV-2 S protein binds to human ACE2 with highaffinity by utilizing the surface plasmon resonance, which is anoptical technique used to determine the molecular interactions andbinding kinetics. Obtaining a large amount of SARS-CoV-2 proteins(e.g. the spike protein) at high-quality is significant for develop-ment of vaccine alternatives or for research purposes. In thisrespect, Herrera et al. reported that ExpiCHO-S cell lines providedenhanced yields of spike proteins (Herrera et al., 2020). To validatethe protein quality, stability and antigenicity, they analyzed theexpressed and purified spike proteins by using the biochemical,biophysical and structural techniques and assays such as cryo-EMPhysica(3D structure, protein conformation), enzyme-linked immunosor-bent assay (ELISA; antigenicity), protein microarray (antigenicity),flow cytometry (binding, specificity), analytical ultracentrifugation(oligomerization), SDS-page (protein size, molecular mass), lightscattering (molecular mass, aggregation), and differential scanningfluorimetry (thermal stability, melting temperature). In anotherstudy associated with the COVID-19 studies, biochemical and bio-physical characterization of the main protease, 3-chymotrypsin-like protease (3CLpro) from SARS-CoV-2 has been recently reported(Ferreira and Rabeh, 2020). Since 3CLpro of SARS-CoV-2 might be aG. Güler, H. Özdemir, D. Omar et al.promising antiviral drug target, its thermodynamic and kineticstability at various pH and salt buffering conditions were studied byusing differential scanning calorimetry, differential scanning fluo-rimetry and circular dichroism (CD) spectroscopy. The far UV-CDspectroscopic data in the 200-280 nm range was used fortracking of secondary structural elements (eg. z-helix. B-sheets)and thus protein structural integrity at various pH and salt buff-ering conditions of 3CLpro. They reported that the protease hasrelatively high thermodynamic stabilities over a wide pH range butis less stable in the presence of salts. It is obvious that biophysical,biochemical, structural, and dynamical characterization of SARS-CoV-2 proteins helps to understand the viral features further, andthus, providing enormous information to discover strategies tocombat COVID-19.3.1. Structure of SARS-CoV-2An RNA virus SARS-CoV-2 exhibits a spherical shape with adiameter of 60-140 nm and has many spikes (9-12 nm long) on itssurface, and thus, it appears like a solar corona revealed by theelectron microscopic data (Zhu et al., 2020), SARS-CoV-2 contains apositive-sense,single-stranded RNA genome. Its genome comprises-29.8 kilobases-long RNA and has 11 open reading frames (ORFs),including ORF1ab, ORF2, ORF3a, ORF4, ORFS, ORF6, ORF7a, ORF7b,ORFS, ORF9 and ORF10 genes (Yoshimoto, 2020) (Fig. 1A). Accord-ingly, ORF1ab gene expresses a large polyprotein which is furthercleaved by proteases into 16 nonstructural proteins (NSPs).including also major enzymes like NSP3 (papain-like proteases,PLP), NSPS (chymotrypsin-like protease, 3CLP), NSP12 (RNA-dependent RNA polymerase, RdRp) and NSP13 (helicase, Hel) (Luket al., 2019; Yoshimoto, 2020), SARS-CoV-2 is made up of four mainstructural proteins, responsible for replication processes and cellentering. These proteins are the spike (S) protein encoded by ORF2,the envelope (E) protein encoded by ORF4, the membrane (M)protein encoded by ORFS, and the nucleocapsid (N) protein enco-ded by ORF9. Besides, the gene fragments distributed among thestructural genes encodes the accessory/helper proteins (Lu et al.,2020; Schoeman and Fielding, 2019; Wu et al., 2020; Yoshimoto,2020). The enveloped structure of SARS-CoV-2 is made up of abilayer lipids and proteins (S glycoprotein, E, M). A ribonucleo-protein core, which consists of the N protein bound to RNA genome,is located inside this viral envelope (Fig. 1B) (Naqvi et al, 2020;Yoshimoto, 2020)The smallest structural protein of SARS-CoV-2 is the E proteinwhich is an integral membrane protein found in the viral mem-brane. It plays a number of key roles in the viral replication such asenvelope formation, viral assembly, and it functions as ion channelsAGENOME5OFFT51 SubuORFIDRAD51-52Junction201SEMIS52 SubunitTNTD CTD 85-485 FP-HR 2 IM IC▬▬▬$2Progress in Biophysics and Molecular Biology 164 (2021) 3-18and interacts with host cell proteins (Li et al., 2020a; Naqvi et al.,2020; Yoshimoto, 2020). The most abundant structural protein isthe M protein which is an integral membrane protein that spans theviral membrane. It interacts with other main viral proteins and hassignificant role in the RNA packaging and viral assembly, shapingthe viral envelope (Naqvi et al., 2020; Tang et al., 2020; Yoshimoto,2020), The N protein is a -54 kDa protein that binds to viral RNAstructurally and assembles into a helical ribonucleocapsid. A recentpublication reported that its N-terminal is the RNA-binding domainwhile its C-terminal domain is responsible for homodimerization(PDB ID: 6WZO), very similar to that of SARS-CoV and MERS-CoV.and it forms large oligomers (tetramers) likely through nucleicacid-protein and protein-protein interactions (Ye et al., 2020). Thisnucleocapsid phosphoprotein is involved in the transcription,replication and packaging of the viral RNA (Naqvi et al., 2020;Schoeman and Fielding, 2019; Ye et al., 2020; Yoshimoto, 2020), Thespike (S) proteins coated with polysaccharides are glycoproteinsthat a large number of S proteins protrude like a pedal-shapedspike on the surface of the virus envelope (Fig. 2A). The S proteinhas 2 vital subunits for binding (S1 subunit) and fusion (S2 subunit)with the host cell. Briefly, the S protein facilities the entry into thehuman cells by attaching to a specific receptor (ACE2) located onthe surface of the host cell (Fig. 2B). Those main structural proteinsaddressed above have collateral effects on the viral infection, andthus, they can be considered as potential drug targets as well. In thefollowing sections of biophysical parts, the characteristics of spikeprotein can be comprehended in a more detailed way, which canhelp with the understanding of the connection of the virus with thehuman cells.3.2. Structure of spike (S) protein2017Currently, it is well known that the COVID-19 infection initiateswith the interaction of SARS-CoV-2 spike (S) protein (termed SARS-CoV-2 S) with human cells as a first step (Fig. 2B). The S proteins ofboth SARS-CoV-2 and SARS-CoV bind to human ACE2 receptor athigh affinities in the nanomolar range to enter and invade thetarget human cells (Walls et al., 2020; Wang et al., 2020b; Wrappet al., 2020). Thus, SARS-CoV-2 S protein is an essential target fortherapeutic, diagnostic and biological research.SARS-CoV-2 S protein has a high amino acid sequence identitywith the S glycoproteins of SARS-CoV (76%) and BatCoV-RaTG13(97%) (Walls et al, 2020; Yoshimoto, 2020; Zhou et al., 2020).SARS-CoV-2 has a longer spike protein with a length of 1273 aminoacids in comparison to both SARS-CoV and MERS-CoV (Lu et al.,2020). A recent cryo-EM structural data revealed that SARS-CoV-2S protein has a total structural weight of -438 kDa (Pdb ID:BProtein (M)RNA-ASpike Protein (5)theo thProtein (N)Envelope Protein (E)Fig. 1. Schematic representations of SARS-CoV-2 genome and structure. (A) Single-stranded RNA genome with a length of -29.8 kb, showing the spike protein in detail. (B) Structureof SARS-CoV-2, demonstrating its main structural proteins which are spike protein, membrane protein, envelope protein, and nucleocapsid protein. (Created with BioRender G. Güler, H. Ozdemir, D. Omar et al.ARBM receptor binding52 sub (fin)51 subunit (BDreceptor-bindingdomain)Viralmembraneeruscellular tall6VXX) (Walls et al., 2020). The S protein, a heavily-glycosylatedtype I transmembrane protein, mediates attachment and entryinto target cells. This large homotrimeric S protein, decorated with22 N-linked glycans per protomer (Walls et al., 2020; Watanabeet al., 2020), is known for making protrusions like a crown on theviral surface. The S protein comprises of three parts: (f) an ecto-domain having a triangular cross-section with a length of 160 A (ii)a single-pass transmembrane anchor, and (iii) an intracellular tail(Li, 2016; Walls et al., 2020) (Fig. 2A). The ectodomain segment ofhomotrimeric S protein has S1 and S2 functional subunits in eachmonomer, which are associated with the receptor recognition andmembrane fusion, respectively (Fig. 3A and B). Accordingly, the S1subunit exhibiting a V-shaped structure comprises a receptorbinding domain (RBD) that binds to the receptor protein ACE2located on the host cell surface, providing viral attachment. This isfollowed by the host cell membrane fusion through the S2 subunitso that the viral genomes can enter into target cells (Cascella et al.,2020; Li, 2016; Mathewson et al., 2008; Paul S. and Stanley, 2007;Walls et al., 2020). The S2 subunit harbours mainly a-helical sec-ondary structures (Fig. 3B). It contains a fusion peptide (FP) region,heptad repeats (HR1 and HR2), a solely 40% identity with otherSARS-CoVs (Cascella et al., 2020; Walls et al., 2020). Thus, the S2subunit and the conserved motif in the S1 subunit can be thoughtas potential targets for neutralizing transmembrane domain (TM)and cytoplasmic domain, which is conserved in SARS-CoV-2sharing 88% sequence identity, whereas the amino acid sequenceof the receptor-binding domain in S1 shows antibodies againstCOVID-19.BRecent cryo-EM data (Carrique et al., 2020; Toelzer et al., 2020)have revealed bound unsaturated fatty acids on the RBD of thetrimeric S protein. It was reported that the RBDs of trimeric SARS-CoV-2 S protein tightly and specifically binds to the essential freefatty acid linoleic acid in three composite binding pockets (Toelzeret al., 2020). Again recently reported, the acyl chains of unsaturatedfatty acids bind to a hydrophobic pocket in one RBD of the trimericS protein while the polar headgroups attach to an adjacent RBD,showing that lipid-like molecules modulate the S protein stability.Thereby, it was proposed in both studies that these binding pocketscould be a promising target for development of small molecule-inhibitors or other therapeutics against SARS-CoV-2 (Carriqueet al., 2020; Toelzer et al., 2020).SARS-CoV-2Progress in Biophysics and Molecular Biology 164 (2021) 3-18Host cellSP(8)AttachmentACE2Fig. 2. Schematic representations of SARS-CoV-2 spike protein and its attachment to host cell. (A) Trimeric spike protein of SARS-CoV-2, showing its functional subunits 51 (receptorbinding domain) and 52 (membrane-fusion domain). (B) SARS-CoV-2 spike protein, representing its attachment to specific receptor angiotensin converting enzyme 2 (ACE2) locatedon the surface of the host cell for cell entry. (Created with BioRender.com)Cellmembrane3.3. The S1/S2 junction and S2' cleavage siteA cascade of events occurring during receptor attachment andproteolytic processing of trimeric S protein is required for cellularentry of SARS-CoV-2. The S protein is cleaved into S1 and S2 sub-units by proteases on the host cell membrane. Significantly, a furincleavage site was determined at the boundary between the S1/S2subunits of the SARS-CoV-2 S protein, cleaved during S biogenesis(Walls et al., 2020). This S1/S2 junction is located in a disordered,solvent-exposed loop structure of the S protein (Wrapp et al., 2020)(Fig. 3B). This polybasic furin cleavage site (amino acid sequence:QTQTNSPRRARSVASQSIIA) is absent in the S protein of SARS-CoV(Yoshimoto, 2020). Additionally, the S2 subunit involves a prote-ase cleavage site (called S2' site) at the upstream of the hydro-phobic fusion peptide. The S₂' cleavage site of SARS-CoV-2 S proteinwas found similar to that of SARS-CoV (Hoffmann et al., 2020).Recently determined that the S protein is cleaved at the S1/S2 andS₂' sites by host cell proteases such as furin and TMPRSS2 to activatethe spike protein for a tight binding to the ACE2 receptor and formembrane fusion through multiple conformational alterations.This is crucial for expanding of SARS-CoV-2 cell and modulation oftropism, transmissibility and pathogenicity (Hoffmann et al., 2020;Walls et al., 2020). It was also explicitly showed that SARS-CoV-2requires both host cell ACE2 receptor and serine proteaseTMPRSS2 for S protein priming to enter into the host cell, and thus,it was suggested that SARS-CoV-2 can be blocked by usingTMPRSS2 inhibitors against COVID-19 (Hoffmann et al., 2020).3.4. Conformational changes of S protein (open/closed or up/downstates)The trimeric S protein exhibits concerted conformationalchanges crucial for receptor binding and membrane fusion.Recently, open and closed conformations of SARS-CoV-2 spikeglycoprotein has been detected (Walls et al., 2020). Accordingly, inthe closed state of S trimers, the recognition motifs (RBMs) in theRBD of the S1 subunit are buried at the interface between proto-mers (Fig. 3A). However, in the open conformation of S1 at thetrimer apex, the RBMs are exposed (Fig. 3B) which is required forACE2 interaction followed by S2 conformational alterations in aconcerted manner for protease cleavage at the S₂' site, membranefusion and entry into target cells. Hence, Walls et al. (2020) pro-posed that trimeric S proteins of highly pathogenic human coro-naviruses should undergo partially opened states, but humanG. Güler, H. Özdemir, D. Omar et alAProtomer 3Protomer 1,*******Viral membraneProtomer 2BProtomer 1(up conformation)$1 bindingsubunitNTD52 fusion Furin cleavagesubunitsite (51/5252 sitecoronaviruses with common colds should have largely closedtrimeric S proteins (Walls et al., 2020). In line with this study, thereceptor-accessible (open or up conformation) and receptor-inaccessible (closed or down conformation) states of S trimershave been structurally determined (Wrapp et al., 2020) (Fig. 3C). Inthe prefusion conformation of S trimer, a single receptor-bindingdomain (RBD) of S1 in one protomer rotates up (receptor-acces-sible state) and becomes exposed to receptor binding (Fig. 3A). Thisrenders the S trimer less stable, and results in a highly stablepostfusion conformation of the S2 subunit and membrane fusion. Inthe closed or down conformation, RBD of S1 is angled through thecentral trimeric cavity (Wrapp et al., 2020). Recently, a stabilizedprefusion SARS-CoV-2 spike ectodomain has been designed toenhance the yield and stability so that it can be a promisingcandidate for vaccine and diagnostic developments (Hsieh et al..2020). Additionally, enhanced yields of high quality SARS-CoV-2 Sproteins (recombinant S proteins) that have appropriatebiochemical and biophysical properties were generated for in-vestigations in both clinical and basic science (Herrera et al., 2020).3.5. ACE2 receptor recognition by spike proteinSARS-CoV-2 S protein binds to human cell receptor ACE2 with ahigh affinity of 14.7 nM analyzed by using surface plasmon reso-nance, which is much higher than that of SARS-CoV (Wrapp et al..2020), ACE2 is a type I transmembrane x-helical protein. It com-prises the N-terminal peptidase domain (PD) and C-terminal.collectrin-like domain (CLD), involving a small extracellulardomain, a long linker as well as a single TM helix. Recently reportedthat two S protein trimers can simultaneously bind to a humanACE2 homodimer, derived from the cryo-EM data of RBD-ACE2-BOAT1 ternary complex, existing as a dimer of heterodimers (Yanet al., 2020). Accordingly, mainly the neck domain (residues from616 to 726) and also the peptidase domain (PD, residues from Ser19to Asp615) of ACE2 contribute to this stable dimerization (withoutamino acid transporter BOAT1 contribution), through many polarinteractions. Existence of the weak interaction at the PD dimerwwwwwwinterface reveals its ability to transition to an open conformation,leading to a -25 A-separation: thus, the un conformation (open) ofREMRBD (up)********************Viral membrane***********Progress in Biophysics and Molecular Biology 164 (2021) 3-18CRBDdownRBDFig. 3. A 3D structure of homotrimeric SARS-CoV-2 S ectodomain. (A) The RBD on each protomer of trimeric S protein exhibits down conformation (closed) in the prefusion state(PDB ID: 6VXX). (B) The RBD of protomer 1 (green) of homotrimeric S protein is in the up conformation (open state) (PDB: 6VSB). (C) Top view of homotrimeric S glycoprotein,showing the RBDs in the up and down conformations (PDB ID: GVSB), Attached carbohydrates are shown in blue-cubic shapes. Figures were reproduced from protein data bank(PDB), RBD, receptor binding domain; KBM: receptor binding motif; NTD, N-terminal domainRBD up conformation[receptor-accessible state)RDB in S1 is necessary to bind to ACE2 (Yan et al., 2020), which is inline with the results of other recent biophysical studies (Walls et al.,2020; Wrapp et al., 2020). For recognition, the interaction occursmainly between an extended loop in the receptor-binding motif(RBM) in the RBD of SARS-CoV-2 S protein (Gln498, Thr500,Asn501, Lys417, Tyr453, Gln474) and the N-terminal 1 helix of theextracellular PD of ACE2 (Tyr41, Gln42, Lys353, Arg357, Asp30.His34, Gln24) mainly through polar residues that undergo H-bonding (Yan et al., 2020) (Fig. 4A and B). In line with this result,recently also revealed that the RBD of SARS-CoV-2 comprises thesecondary structures of five antiparallel ß-sheets, two short a-he-lices and loops (Lan et al., 2020). In the RBD of S1 subunit, short 85,86, 24, 25 and loops constitute the RBM. This RBM is an extendedregion which includes most of the ACE2-interacting residues. Basedon this X-ray crystallographic structure of the SARS-CoV-2RBD-ACE2 complex, 17 residues in the SARS-CoV-2 RBD havenetworks with 20 residues of the ACE2 receptor through mainlyhydrophilic interactions such as H-bonding and salt bridges. Exis-tence of high structural similarity in the RBD-ACE2 interfacesstrongly shows convergent evolutionary relationship betweenSARS-CoV-2 and SARS-CoV for strong ACE2 binding (Lan et al.2020). In agreement with these results, recent studies have re-ported very similar and complimentary data, including the struc-tural features and hotspots at the RBD-ACE2 interface althoughusage of different methodologies and sampling procedures (Shanget al., 2020; Wang et al., 2020b). Accordingly, the binding interfacebetween the SARS-CoV-2 RBM and ACE2 forms a larger buriedsurface, includes a series of hydrophilic residues that makes strongpolar contacts, and contains van der Waals contacts and aromaticinteractions (Shang et al., 2020; Wang et al., 2020b). It is obviouslyclear from the biophysical sight that SARS-CoV-2 has importantinterconnections with ACE2, which will be addressed in thebiochemical part through considering its function in Renin-Angiotensin-System.

Question

Read Section 3  to 3.5 and answer the ff:-What biomolecule contains the genetic information of SARS-CoV-2? Be specific.-Describe the structure of the SARS-CoV-2.-What are the four main structural proteins in SARS-CoV-2? Briefly explain what each protein does.-How does SARS-CoV-2 bind to the host cell? Provide some evidences to support your answer.-What proteins can be targeted for therapeutic purposes (i.e. vaccines or antiviral drugs)? G. Galer, H. Özdemir, D. Omar et alinformation, Coronaviruses have infectious, non-segmented and asingle positive-sense RNA molecule. Coronaviruses and Torovirusesare within the virus family, Coronavidiae. While coronaviruses havepathogenic capacity on both animals and humans, Toroviruses areone of the main reasons for animal diarrhea (Peiris, 2012), Coro-naviruses can be divided into 4 groups known as alpha, beta, gammaand delta, and people commonly get infected by alpha and betacoronaviruses as known as: 229 E, NL63, OC43, and HKU1 (CDC.2020). They are well known for their positive single-strandedRNA genomes of approximately 30 kb, enveloped with nucleo-capsid (Perlman and Netland, 2009). Recent studies have alsoshown that current coronavirus threatening public health belongsto betacoronavirus (Huang et al., 2020). It is really important tounderstand the nature of a virus to come up with the right treat-ment, thus, the studies regarding its pathogenesis carry a valid role.To find a relation between SARS-CoV-2 and other coronaviruses, astudy calculated the sequence identity by collecting samples fromdifferent types. It was revealed that samples from COVID-19infected patients presented a close relationship with two bat-derived coronaviruses: bat-SL-COVZC45 and bat-SL-CoVZXC21. Infact, SARS-CoV-2 showed 88% identity with the two bat-derivedcoronaviruses. In comparison to these viruses, the associationsbetween SARS-CoV-2 and SARS-CoV as well as MERS-CoV weremore distant. While SARS-CoV showed -79% identity with SARS-CoV-2, MERS-CoV showed only -50% identity with SARS-CoV-2(Lu et al., 2020). It was also reported that SARS-CoV-2 is 96%identical at the whole-genome level to another bat coronavirus.(BatCoV-RaTG13) (Zhou et al., 2020). This close relationship mayprovide an evidence for SARS-CoV-2 to be originated in bats.With the spread of the virus, new variants and mutations havestarted to become a problem in some regions. In 2020 December, anew variant appeared in the UK; it was revealed that this newvariant was associated with the spike protein of the virus. In lateDecember, it caused increased number of cases in the southeast ofEngland. Authorities stated that the new mutation would not causea major problem within the vaccine, as the vaccine affects manyregions in the spike protein (Wise, 2020). A matched cohort studyrevealed the mortality rate to be slightly higher in the new strain(Challen et al., 2021). Another variant named 501Y.V2 was found inSouth Africa on December 18, 2020. It was discovered that this newvariant had spread to various provinces. Furthermore, this variantwas found to have 3 mutations in the spike protein (Tang et al.,ang et2021: &#34;WHO | SARS-CoV-2 Variants,&#34; n. d.). Although the researchis still ongoing, according to a study, South African strain may bemore transmissible (Tegally et al., 2020),Coronavirus has one of the best studied genome structures sofar, and exhibits a high mutation rate (Cui et al, 2019). Mutations inthis novel virus significantly affected the chain of transmission.Although SARS-CoV-2 contains amino acid mutations in itsreceptor-binding domain (Lu et al., 2020), both SARS-CoV andSARS-CoV-2 use their spike proteins to recognize the angiotensinconverting enzyme 2 (ACE2) as a functional receptor on the targetcell for entry (Hoffmann et al., 2020; Lan et al., 2020; Letko et al..2020; Shang et al., 2020; Walls et al., 2020; Wang et al., 2020b;Yan et al., 2020). Recently, biophysical, and biochemical propertiesof SARS-CoV-2 have been studied in detail, which will be addressedin the following Sections 3 and 4.3. Structural and functional features of SARS-CoV-2Phylogenetic analyses revealed that SARS-CoV-2 belongs to thebetacoronavirus category of the Coronaviridae family. The corona-virus disease 2019 (COVID-19), rapidly spreading worldwide, iscaused by this novel RNA virus SARS-CoV-2. To fight this globalcrisis, effective treatment and vaccine alternatives against COVID-Progress in Biophysics and Molecular Biology 164 (2021) 3-1819 are urgently required. Obviously, understanding the structuraland functional features, dynamics and receptor recognitionmechanism of SARS-CoV-2 is the first crucial step to develop theeffective antiviral drug agents, novel targeted treatments, smallmolecular inhibitors, blocking antibodies, other therapeutics aswell as to design an effective preventive vaccine against COVID-19.Knowing the structures and interactions on the atomic level willguide to identify potential targets by applying, for instance, in silicostructure-assisted drug design or molecular docking procedures tofind new drugs or to repurpose already approved drugs (Estrada,2020; Hoffmann et al., 2020; Jin et al., 2020b). Hence, so farstructural and functional relationship of SARS-CoV-2 proteins havebeen extensively studied by using biophysical techniques (e.g.cryogenic electron microscopy (Cryo-EM), X-ray crystallography),along with biochemical and biological assays (Lan et al., 2020;Shang et al., 2020; Walls et al., 2020; Wang et al., 2020b; Wrappet al., 2020; Yan et al., 2020). Further studies on SARS-CoV-2 arestill ongoing with increasing tendency to have integrated knowl-edge about molecular basis of recognition, molecular and atomicinteractions as well as conformational changes occurring duringviral attachment and entering into human cells.Recently, biophysical and biochemical techniques have beenapplied for characterization of SARS-CoV-2 in the COVID-19 studies.Importantly, Cryo-EM (using deflection of electrons from frozenprotein samples at liquid nitrogen temperatures) and X-ray crys-tallography (using scattering of X-rays from well-ordered proteincrystals) have been used to determine the 3D structure of SARS-CoV-2 proteins at atomic resolution in a few Angstrom (A) range.Later on, the atomic coordinates and maps of the protein 3Dstructures have been deposited in the Protein Data Bank (PDB),freely available to global community. In this regard, Lan et al.determined the crystal structure of the receptor-binding domain(RBD) of SARS-CoV-2 spike protein bound to the cell receptor ACE2at 2.45 A resolution (PDB ID: 6M0J) by using X-ray diffraction data(Lan et al., 2020). They also identified the amino acid residues of theSARS-CoV-2 RBD, essential for the ACE2 binding. Walls et al.determined the cryo-EM structures of the SARS-CoV-2 S ectodo-main trimer in the closed (2.8 A resolution, PDB ID: 6VXX) andpartially opened (3.2 A resolution, PDB ID: 6VYB) conformations(Walls et al., 2020). In another work, Wrapp et al. determined thecryo-EM structure of the SARS-CoV-2 spike protein in the prefusionconformation at 3.46 A resolution and identified that one of thethree receptor-binding domains is 'up' in a receptor-accessibleconformation (PDB ID: 6VSB) (Wrapp et al., 2020). They alsoshowed that SARS-CoV-2 S protein binds to human ACE2 with highaffinity by utilizing the surface plasmon resonance, which is anoptical technique used to determine the molecular interactions andbinding kinetics. Obtaining a large amount of SARS-CoV-2 proteins(e.g. the spike protein) at high-quality is significant for develop-ment of vaccine alternatives or for research purposes. In thisrespect, Herrera et al. reported that ExpiCHO-S cell lines providedenhanced yields of spike proteins (Herrera et al., 2020). To validatethe protein quality, stability and antigenicity, they analyzed theexpressed and purified spike proteins by using the biochemical,biophysical and structural techniques and assays such as cryo-EMPhysica(3D structure, protein conformation), enzyme-linked immunosor-bent assay (ELISA; antigenicity), protein microarray (antigenicity),flow cytometry (binding, specificity), analytical ultracentrifugation(oligomerization), SDS-page (protein size, molecular mass), lightscattering (molecular mass, aggregation), and differential scanningfluorimetry (thermal stability, melting temperature). In anotherstudy associated with the COVID-19 studies, biochemical and bio-physical characterization of the main protease, 3-chymotrypsin-like protease (3CLpro) from SARS-CoV-2 has been recently reported(Ferreira and Rabeh, 2020). Since 3CLpro of SARS-CoV-2 might be aG. Güler, H. Özdemir, D. Omar et al.promising antiviral drug target, its thermodynamic and kineticstability at various pH and salt buffering conditions were studied byusing differential scanning calorimetry, differential scanning fluo-rimetry and circular dichroism (CD) spectroscopy. The far UV-CDspectroscopic data in the 200-280 nm range was used fortracking of secondary structural elements (eg. z-helix. B-sheets)and thus protein structural integrity at various pH and salt buff-ering conditions of 3CLpro. They reported that the protease hasrelatively high thermodynamic stabilities over a wide pH range butis less stable in the presence of salts. It is obvious that biophysical,biochemical, structural, and dynamical characterization of SARS-CoV-2 proteins helps to understand the viral features further, andthus, providing enormous information to discover strategies tocombat COVID-19.3.1. Structure of SARS-CoV-2An RNA virus SARS-CoV-2 exhibits a spherical shape with adiameter of 60-140 nm and has many spikes (9-12 nm long) on itssurface, and thus, it appears like a solar corona revealed by theelectron microscopic data (Zhu et al., 2020), SARS-CoV-2 contains apositive-sense,single-stranded RNA genome. Its genome comprises-29.8 kilobases-long RNA and has 11 open reading frames (ORFs),including ORF1ab, ORF2, ORF3a, ORF4, ORFS, ORF6, ORF7a, ORF7b,ORFS, ORF9 and ORF10 genes (Yoshimoto, 2020) (Fig. 1A). Accord-ingly, ORF1ab gene expresses a large polyprotein which is furthercleaved by proteases into 16 nonstructural proteins (NSPs).including also major enzymes like NSP3 (papain-like proteases,PLP), NSPS (chymotrypsin-like protease, 3CLP), NSP12 (RNA-dependent RNA polymerase, RdRp) and NSP13 (helicase, Hel) (Luket al., 2019; Yoshimoto, 2020), SARS-CoV-2 is made up of four mainstructural proteins, responsible for replication processes and cellentering. These proteins are the spike (S) protein encoded by ORF2,the envelope (E) protein encoded by ORF4, the membrane (M)protein encoded by ORFS, and the nucleocapsid (N) protein enco-ded by ORF9. Besides, the gene fragments distributed among thestructural genes encodes the accessory/helper proteins (Lu et al.,2020; Schoeman and Fielding, 2019; Wu et al., 2020; Yoshimoto,2020). The enveloped structure of SARS-CoV-2 is made up of abilayer lipids and proteins (S glycoprotein, E, M). A ribonucleo-protein core, which consists of the N protein bound to RNA genome,is located inside this viral envelope (Fig. 1B) (Naqvi et al, 2020;Yoshimoto, 2020)The smallest structural protein of SARS-CoV-2 is the E proteinwhich is an integral membrane protein found in the viral mem-brane. It plays a number of key roles in the viral replication such asenvelope formation, viral assembly, and it functions as ion channelsAGENOME5OFFT51 SubuORFIDRAD51-52Junction201SEMIS52 SubunitTNTD CTD 85-485 FP-HR 2 IM IC▬▬▬$2Progress in Biophysics and Molecular Biology 164 (2021) 3-18and interacts with host cell proteins (Li et al., 2020a; Naqvi et al.,2020; Yoshimoto, 2020). The most abundant structural protein isthe M protein which is an integral membrane protein that spans theviral membrane. It interacts with other main viral proteins and hassignificant role in the RNA packaging and viral assembly, shapingthe viral envelope (Naqvi et al., 2020; Tang et al., 2020; Yoshimoto,2020), The N protein is a -54 kDa protein that binds to viral RNAstructurally and assembles into a helical ribonucleocapsid. A recentpublication reported that its N-terminal is the RNA-binding domainwhile its C-terminal domain is responsible for homodimerization(PDB ID: 6WZO), very similar to that of SARS-CoV and MERS-CoV.and it forms large oligomers (tetramers) likely through nucleicacid-protein and protein-protein interactions (Ye et al., 2020). Thisnucleocapsid phosphoprotein is involved in the transcription,replication and packaging of the viral RNA (Naqvi et al., 2020;Schoeman and Fielding, 2019; Ye et al., 2020; Yoshimoto, 2020), Thespike (S) proteins coated with polysaccharides are glycoproteinsthat a large number of S proteins protrude like a pedal-shapedspike on the surface of the virus envelope (Fig. 2A). The S proteinhas 2 vital subunits for binding (S1 subunit) and fusion (S2 subunit)with the host cell. Briefly, the S protein facilities the entry into thehuman cells by attaching to a specific receptor (ACE2) located onthe surface of the host cell (Fig. 2B). Those main structural proteinsaddressed above have collateral effects on the viral infection, andthus, they can be considered as potential drug targets as well. In thefollowing sections of biophysical parts, the characteristics of spikeprotein can be comprehended in a more detailed way, which canhelp with the understanding of the connection of the virus with thehuman cells.3.2. Structure of spike (S) protein2017Currently, it is well known that the COVID-19 infection initiateswith the interaction of SARS-CoV-2 spike (S) protein (termed SARS-CoV-2 S) with human cells as a first step (Fig. 2B). The S proteins ofboth SARS-CoV-2 and SARS-CoV bind to human ACE2 receptor athigh affinities in the nanomolar range to enter and invade thetarget human cells (Walls et al., 2020; Wang et al., 2020b; Wrappet al., 2020). Thus, SARS-CoV-2 S protein is an essential target fortherapeutic, diagnostic and biological research.SARS-CoV-2 S protein has a high amino acid sequence identitywith the S glycoproteins of SARS-CoV (76%) and BatCoV-RaTG13(97%) (Walls et al, 2020; Yoshimoto, 2020; Zhou et al., 2020).SARS-CoV-2 has a longer spike protein with a length of 1273 aminoacids in comparison to both SARS-CoV and MERS-CoV (Lu et al.,2020). A recent cryo-EM structural data revealed that SARS-CoV-2S protein has a total structural weight of -438 kDa (Pdb ID:BProtein (M)RNA-ASpike Protein (5)theo thProtein (N)Envelope Protein (E)Fig. 1. Schematic representations of SARS-CoV-2 genome and structure. (A) Single-stranded RNA genome with a length of -29.8 kb, showing the spike protein in detail. (B) Structureof SARS-CoV-2, demonstrating its main structural proteins which are spike protein, membrane protein, envelope protein, and nucleocapsid protein. (Created with BioRender G. Güler, H. Ozdemir, D. Omar et al.ARBM receptor binding52 sub (fin)51 subunit (BDreceptor-bindingdomain)Viralmembraneeruscellular tall6VXX) (Walls et al., 2020). The S protein, a heavily-glycosylatedtype I transmembrane protein, mediates attachment and entryinto target cells. This large homotrimeric S protein, decorated with22 N-linked glycans per protomer (Walls et al., 2020; Watanabeet al., 2020), is known for making protrusions like a crown on theviral surface. The S protein comprises of three parts: (f) an ecto-domain having a triangular cross-section with a length of 160 A (ii)a single-pass transmembrane anchor, and (iii) an intracellular tail(Li, 2016; Walls et al., 2020) (Fig. 2A). The ectodomain segment ofhomotrimeric S protein has S1 and S2 functional subunits in eachmonomer, which are associated with the receptor recognition andmembrane fusion, respectively (Fig. 3A and B). Accordingly, the S1subunit exhibiting a V-shaped structure comprises a receptorbinding domain (RBD) that binds to the receptor protein ACE2located on the host cell surface, providing viral attachment. This isfollowed by the host cell membrane fusion through the S2 subunitso that the viral genomes can enter into target cells (Cascella et al.,2020; Li, 2016; Mathewson et al., 2008; Paul S. and Stanley, 2007;Walls et al., 2020). The S2 subunit harbours mainly a-helical sec-ondary structures (Fig. 3B). It contains a fusion peptide (FP) region,heptad repeats (HR1 and HR2), a solely 40% identity with otherSARS-CoVs (Cascella et al., 2020; Walls et al., 2020). Thus, the S2subunit and the conserved motif in the S1 subunit can be thoughtas potential targets for neutralizing transmembrane domain (TM)and cytoplasmic domain, which is conserved in SARS-CoV-2sharing 88% sequence identity, whereas the amino acid sequenceof the receptor-binding domain in S1 shows antibodies againstCOVID-19.BRecent cryo-EM data (Carrique et al., 2020; Toelzer et al., 2020)have revealed bound unsaturated fatty acids on the RBD of thetrimeric S protein. It was reported that the RBDs of trimeric SARS-CoV-2 S protein tightly and specifically binds to the essential freefatty acid linoleic acid in three composite binding pockets (Toelzeret al., 2020). Again recently reported, the acyl chains of unsaturatedfatty acids bind to a hydrophobic pocket in one RBD of the trimericS protein while the polar headgroups attach to an adjacent RBD,showing that lipid-like molecules modulate the S protein stability.Thereby, it was proposed in both studies that these binding pocketscould be a promising target for development of small molecule-inhibitors or other therapeutics against SARS-CoV-2 (Carriqueet al., 2020; Toelzer et al., 2020).SARS-CoV-2Progress in Biophysics and Molecular Biology 164 (2021) 3-18Host cellSP(8)AttachmentACE2Fig. 2. Schematic representations of SARS-CoV-2 spike protein and its attachment to host cell. (A) Trimeric spike protein of SARS-CoV-2, showing its functional subunits 51 (receptorbinding domain) and 52 (membrane-fusion domain). (B) SARS-CoV-2 spike protein, representing its attachment to specific receptor angiotensin converting enzyme 2 (ACE2) locatedon the surface of the host cell for cell entry. (Created with BioRender.com)Cellmembrane3.3. The S1/S2 junction and S2' cleavage siteA cascade of events occurring during receptor attachment andproteolytic processing of trimeric S protein is required for cellularentry of SARS-CoV-2. The S protein is cleaved into S1 and S2 sub-units by proteases on the host cell membrane. Significantly, a furincleavage site was determined at the boundary between the S1/S2subunits of the SARS-CoV-2 S protein, cleaved during S biogenesis(Walls et al., 2020). This S1/S2 junction is located in a disordered,solvent-exposed loop structure of the S protein (Wrapp et al., 2020)(Fig. 3B). This polybasic furin cleavage site (amino acid sequence:QTQTNSPRRARSVASQSIIA) is absent in the S protein of SARS-CoV(Yoshimoto, 2020). Additionally, the S2 subunit involves a prote-ase cleavage site (called S2' site) at the upstream of the hydro-phobic fusion peptide. The S₂' cleavage site of SARS-CoV-2 S proteinwas found similar to that of SARS-CoV (Hoffmann et al., 2020).Recently determined that the S protein is cleaved at the S1/S2 andS₂' sites by host cell proteases such as furin and TMPRSS2 to activatethe spike protein for a tight binding to the ACE2 receptor and formembrane fusion through multiple conformational alterations.This is crucial for expanding of SARS-CoV-2 cell and modulation oftropism, transmissibility and pathogenicity (Hoffmann et al., 2020;Walls et al., 2020). It was also explicitly showed that SARS-CoV-2requires both host cell ACE2 receptor and serine proteaseTMPRSS2 for S protein priming to enter into the host cell, and thus,it was suggested that SARS-CoV-2 can be blocked by usingTMPRSS2 inhibitors against COVID-19 (Hoffmann et al., 2020).3.4. Conformational changes of S protein (open/closed or up/downstates)The trimeric S protein exhibits concerted conformationalchanges crucial for receptor binding and membrane fusion.Recently, open and closed conformations of SARS-CoV-2 spikeglycoprotein has been detected (Walls et al., 2020). Accordingly, inthe closed state of S trimers, the recognition motifs (RBMs) in theRBD of the S1 subunit are buried at the interface between proto-mers (Fig. 3A). However, in the open conformation of S1 at thetrimer apex, the RBMs are exposed (Fig. 3B) which is required forACE2 interaction followed by S2 conformational alterations in aconcerted manner for protease cleavage at the S₂' site, membranefusion and entry into target cells. Hence, Walls et al. (2020) pro-posed that trimeric S proteins of highly pathogenic human coro-naviruses should undergo partially opened states, but humanG. Güler, H. Özdemir, D. Omar et alAProtomer 3Protomer 1,*******Viral membraneProtomer 2BProtomer 1(up conformation)$1 bindingsubunitNTD52 fusion Furin cleavagesubunitsite (51/5252 sitecoronaviruses with common colds should have largely closedtrimeric S proteins (Walls et al., 2020). In line with this study, thereceptor-accessible (open or up conformation) and receptor-inaccessible (closed or down conformation) states of S trimershave been structurally determined (Wrapp et al., 2020) (Fig. 3C). Inthe prefusion conformation of S trimer, a single receptor-bindingdomain (RBD) of S1 in one protomer rotates up (receptor-acces-sible state) and becomes exposed to receptor binding (Fig. 3A). Thisrenders the S trimer less stable, and results in a highly stablepostfusion conformation of the S2 subunit and membrane fusion. Inthe closed or down conformation, RBD of S1 is angled through thecentral trimeric cavity (Wrapp et al., 2020). Recently, a stabilizedprefusion SARS-CoV-2 spike ectodomain has been designed toenhance the yield and stability so that it can be a promisingcandidate for vaccine and diagnostic developments (Hsieh et al..2020). Additionally, enhanced yields of high quality SARS-CoV-2 Sproteins (recombinant S proteins) that have appropriatebiochemical and biophysical properties were generated for in-vestigations in both clinical and basic science (Herrera et al., 2020).3.5. ACE2 receptor recognition by spike proteinSARS-CoV-2 S protein binds to human cell receptor ACE2 with ahigh affinity of 14.7 nM analyzed by using surface plasmon reso-nance, which is much higher than that of SARS-CoV (Wrapp et al..2020), ACE2 is a type I transmembrane x-helical protein. It com-prises the N-terminal peptidase domain (PD) and C-terminal.collectrin-like domain (CLD), involving a small extracellulardomain, a long linker as well as a single TM helix. Recently reportedthat two S protein trimers can simultaneously bind to a humanACE2 homodimer, derived from the cryo-EM data of RBD-ACE2-BOAT1 ternary complex, existing as a dimer of heterodimers (Yanet al., 2020). Accordingly, mainly the neck domain (residues from616 to 726) and also the peptidase domain (PD, residues from Ser19to Asp615) of ACE2 contribute to this stable dimerization (withoutamino acid transporter BOAT1 contribution), through many polarinteractions. Existence of the weak interaction at the PD dimerwwwwwwinterface reveals its ability to transition to an open conformation,leading to a -25 A-separation: thus, the un conformation (open) ofREMRBD (up)********************Viral membrane***********Progress in Biophysics and Molecular Biology 164 (2021) 3-18CRBDdownRBDFig. 3. A 3D structure of homotrimeric SARS-CoV-2 S ectodomain. (A) The RBD on each protomer of trimeric S protein exhibits down conformation (closed) in the prefusion state(PDB ID: 6VXX). (B) The RBD of protomer 1 (green) of homotrimeric S protein is in the up conformation (open state) (PDB: 6VSB). (C) Top view of homotrimeric S glycoprotein,showing the RBDs in the up and down conformations (PDB ID: GVSB), Attached carbohydrates are shown in blue-cubic shapes. Figures were reproduced from protein data bank(PDB), RBD, receptor binding domain; KBM: receptor binding motif; NTD, N-terminal domainRBD up conformation[receptor-accessible state)RDB in S1 is necessary to bind to ACE2 (Yan et al., 2020), which is inline with the results of other recent biophysical studies (Walls et al.,2020; Wrapp et al., 2020). For recognition, the interaction occursmainly between an extended loop in the receptor-binding motif(RBM) in the RBD of SARS-CoV-2 S protein (Gln498, Thr500,Asn501, Lys417, Tyr453, Gln474) and the N-terminal 1 helix of theextracellular PD of ACE2 (Tyr41, Gln42, Lys353, Arg357, Asp30.His34, Gln24) mainly through polar residues that undergo H-bonding (Yan et al., 2020) (Fig. 4A and B). In line with this result,recently also revealed that the RBD of SARS-CoV-2 comprises thesecondary structures of five antiparallel ß-sheets, two short a-he-lices and loops (Lan et al., 2020). In the RBD of S1 subunit, short 85,86, 24, 25 and loops constitute the RBM. This RBM is an extendedregion which includes most of the ACE2-interacting residues. Basedon this X-ray crystallographic structure of the SARS-CoV-2RBD-ACE2 complex, 17 residues in the SARS-CoV-2 RBD havenetworks with 20 residues of the ACE2 receptor through mainlyhydrophilic interactions such as H-bonding and salt bridges. Exis-tence of high structural similarity in the RBD-ACE2 interfacesstrongly shows convergent evolutionary relationship betweenSARS-CoV-2 and SARS-CoV for strong ACE2 binding (Lan et al.2020). In agreement with these results, recent studies have re-ported very similar and complimentary data, including the struc-tural features and hotspots at the RBD-ACE2 interface althoughusage of different methodologies and sampling procedures (Shanget al., 2020; Wang et al., 2020b). Accordingly, the binding interfacebetween the SARS-CoV-2 RBM and ACE2 forms a larger buriedsurface, includes a series of hydrophilic residues that makes strongpolar contacts, and contains van der Waals contacts and aromaticinteractions (Shang et al., 2020; Wang et al., 2020b). It is obviouslyclear from the biophysical sight that SARS-CoV-2 has importantinterconnections with ACE2, which will be addressed in thebiochemical part through considering its function in Renin-Angiotensin-System.

Accepted Answer

SARS-CoV-2 is an infectious virus that is responsible for the recent COVID pandemic. It is a…