Structural implications of SARS-CoV-2 Surface Glycoprotein N501Y mutation within receptor-binding domain [499-505] – computational analysis of the most frequent Asn501 polar uncharged amino acid mutations

Figures & data

Table 1. Average RMSD ($nm$)/SASA (${nm}^2$) per molecule of N501[Y, T, S] heterodimers.

Heterodimer		N501	N501Y	N501S	N501T
RMSD$(\mathit{nm})$	Avg.	0.223	0.266	0.205	0.214
	S.D.	0.031	0.047	0.032	0.04
SASA${(\mathit{nm}}^2)$	Avg.	359.56	364.93	364.66	360
	S.D.	3.6473	3.3889	3.2842	3.4156

*Avg, average values; S.D., standard deviation.

Figure 1. Backbone deviation analysis of N501[Y, T, S] hetero dimers (Gromacs gmx rms program).

Figure 2. Solubility analysis of N501[Y, T, S] hetero dimers (Gromacs gmx sasa program).

Figure 3. Mean $C_{\alpha }$ fluctuation per residue (S-protein RBD) (Gromacs gmx rmsf program).

Table 2. S-Protein RBD domain [499-505]: ProThrAsn(Tyr)GlyValGlyTyr RMSF analysis.

Position	499	500	501	502	503	504	505
Residue	Pro	Thr	Tyr/Asn	Gly	Val	Gly	Tyr
N501Y $C_{\alpha }$ RMSF (nm)	0.135	0.1657	0.1409	0.1488	0.1544	0.136	0.1159
N501$C_{\alpha }$ RMSF (nm)	0.0978	0.0989	0.0973	0.1027	0.1029	0.0989	0.0858
Difference (nm)	0.0372	0.0668	0.0436	0.0461	0.0515	0.0371	0.0301

Figure 4. S-protein RBD secondary structure prediction (Gromacs gmx do_dssp module).

Note: Time is plotted on the horizontal axis (0–50 ns), while S-protein RBD residues in the range of 1–194 are shown on the vertical axis.

Table 3. Secondary structure assessment.

Range	S-protein RDB motif	N501 (wild type)	N501Y (mutant)
34–38 (Figure 4)	[366-370]: SerValLeuTyrAsn	Stable $\alpha$-helix for t > 38.5 ns	Frequent $\alpha$-helix to π-helix transitions for $t>38.5$ ns
52–55 (Figure 4)	[384-387]: ProThrLysLeu	Turn to $\alpha$-helix shifts during [0–9.25] ns and [25–30] ns	Mainly Turn
171–173 (Figure 4)	[503-505]: ValGlyTyr	$3_{10}$-helix for $t>33$ ns	Turn for $t>33$ ns

Figure 5. Hydrogen bonds dynamics in N501 and N501Y hetero dimers (Gromacs gmx hbond program).

Note: red, number of intermolecular hydrogen bonds in N501Y complex during [0–50] ns MD simulation; green, number of intermolecular hydrogen bonds in N501 complex during [0–50] ns MD simulation.

Table 4. Average number of hydrogen bonds formed in [0–50] ns, wild-type or mutant S-protein RBD [499-505]: ProThrAsn(Tyr)GlyValGlyTyr.

	Number of intermolecular h-bonds, t= [0–50] ns Average ± S.D.*
Domain	S-protein–hACE2	S-Protein [499-505]–hACE2
Wild type (N501)	7.378 ± 1.801	2.186 ± 0.759
Mutant (N501Y)	5.735 ± 1.323	2.375 ± 0.71

*SD, standard deviation.

Table 5. S-protein RBD [499-505]: ProThrAsnGlyValGlyTyr–hACE2 hydrogen bonds dynamics in wild type N501.

N501 (wild type)		hACE2
		Glu37		Tyr41		Lys353		Gly354		Asp355
SARS-CoV-2 S-protein RBD	Thr500			OG112113 HG112114…OH368						OG112113 HG112114… OD25323
				0–50 (ns)	42.3–50 (ns)					0–50 (ns)	42.3–50 (ns)
				8.3%	0.3%					86.8%	98.4%
				0.2901 ± 0.0183 nm	0.313 ± 0.0099 nm					0.2743 ± 0.0165 nm	0.2721 ± 0.0145 nm
	Asn501			ND212130 HD2112131… OH368		ND212130 HD2112131… O5306				ND212130 HD2112131… OD25323
				0–50 (ns)	42.3–50 (ns)	0–50 (ns)	42.3–50 (ns)			0–50 (ns)	42.3–50 (ns)
				(0.3%)	(0%)	(2.3%)	(0.9%)			(1.8%)	(1.4%)
				0.3221 ± 0.019 nm		0.3070 ± 0.0207 nm	0.3283 ± 0.0166 nm			0.3232 ± 0.0196 nm	0.3123 ± 0.0181 nm
	Gly502					N12135 HN12136… O5306		N12135 HN12136… O5313
						0–50 (ns)	42.3–50 (ns)	0–50 (ns)	42.3–50 (ns)
						79.5%	83.1%	3.7%	1%
						0.3031 ± 0.0195 nm	0.3061 ± 0.0193 nm	0.3123 ± 0.0194 nm	0.3036 ± 0.0191 nm
	Tyr505	OH12178 HH12179…OE1 300
		0–50 (ns)	42.3–50 (ns)
		11.7%	6.9%
		0.2867 ± 0.0253 nm	0.3133 ± 0.0242 nm

Note: The impact of a hydrogen bond is measured by means of occupancy – life span of h-bond in % and $r_{DA}$ (donor-acceptor distance, measured in nm). Orange, S-protein donors hydrogen bond to hACE2; shading intensity proportional to hydrogen bond occupancy.

Table 6. S-protein RBD [499-505]: ProThrTyrGlyValGlyTyr–hACE2 hydrogen bonds dynamics in mutant N501Y.

N501Y (mutant)		hACE2
		Glu37		Asp38		Tyr41		Lys353		Asp355
SARS-CoV-2 S-protein RBD	Thr500					OG112113 HG112114…OH368				OG112113 HG112114… OD25323
						0–50 (ns)	42.3–50 (ns)			0–50 (ns)	42.3–50 (ns)
						20.1%	9.1%			66.5%	88.8%
						0.2892 ± 0.0168 nm	0.2852 ± 0.0131 nm			0.2757 ± 0.0169 nm	0.2763 ± 0.0170 nm
	Tyr501			OH12134HH12135… OD1312				NZ5301HZ1 5302…OH12134
				0–50 (ns)	42.3–50 (ns)			0–50 (ns)	42.3–50 (ns)
				3.5%	0%			2%	2.2%
				0.2717 ± 0.0172 nm				0.3017 ± 0.0197 nm	0.3067 ± 0.0228 nm
	Gly502							N12142HN12143… O5306
								0–50 (ns)	42.3–50 (ns)
								98.4%	97.9%
								0.2909 ± 0.0157 nm	0.2915 ± 0.0162 nm
	Tyr505	OH12185HH12186… OE1300/OE2301
		0–50 (ns)	42.3–50 (ns)
		41%	17.5%
		0.2818 ± 0.0223 nm	0.2812 ± 0.0208 nm

Note: The impact of a hydrogen bond is measured by means of occupancy – life span of h-bond in % and $r_{DA}$ (donor-acceptor distance, measured in nm).

Note: Orange, S-protein donors hydrogen bond to hACE2; Blue, hACE2 donors hydrogen bond to S-protein; shading intensity proportional to hydrogen bond occupancy.

Figure 6. Visualization of hydrogen bonds between hACE2 and SARS-CoV-2 spike protein – N501 against N501Y heterodimer drawn in PyMol molecular graphics program.

Note: red, high occupancy of a hydrogen bond; yellow, average occupancy of a hydrogen bond.

Table 7. ${\mathit{Gly}502}_{S-\mathit{Protein}}\mathit{N}-\mathit{H}\dots \mathit{O}=\mathit{C}{\mathit{Lys}353}_{\mathit{hACE}2}$ energy (kcal/mol) in N501 and N501Y heterodimers.

${\mathit{Gly}502}_{\mathit{S}-\mathit{Protein}}\mathit{N}-\mathit{H}\dots \mathit{O}=\mathit{C}{\mathit{Lys}353}_{\mathit{hACE}2}$	${\mathit{r}}_{\mathit{ON},\mathit{avg}}$(Å)	${\mathit{r}}_{\mathit{CH},\mathit{a}}$(Å)	${\mathit{r}}_{\mathit{OH},\mathit{avg}}$(Å)	${\mathit{r}}_{\mathit{CN},\mathit{avg}}$(Å)	Energy (kcal/mol)
[0–50] ns wild type (N501)	3.03053307	3.13261252	2.08334171	4.10371134	3.909532232
[0–50] ns mutant (N501Y)	2.9092403	3.06141174	1.94696323	4.02390412	4.816210332
[42.3–50] ns wild type (N501)	3.06087363	3.16656786	2.11826833	4.13800312	3.739474518
[42.3–50] ns mutant (N501Y)	2.91512583	3.06757616	1.95074172	4.03357616	4.803593311

Note: Eq. 1 was applied to compute hydrogen bond energy.

Data availability

The data that support the findings reported in this paper are available in the Appendix files: RMSD_analysis.xlsx; RMSF_analysis.xlsx; SASA_analysis.xlsx; H_bonds_analysis.xlsx; Gly502_Lys353_H-bond_Energy.xlsx