Adsorption of SARS-CoV-2 Spike (N501Y) RBD to Human Angiotensin-Converting Enzyme 2 at a Lipid/Water Interface

The receptor binding domain (RBD) of spike proteins plays a crucial role in the process of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) attachment to the human angiotensin-converting enzyme 2 (ACE2). The N501Y mutation and later mutations introduced extra positive charges on the spike RBD and resulted in higher transmissibility, likely due to stronger binding with the highly negatively charged ACE2. Consequently, many studies have been devoted to understanding the molecular mechanism of spike protein binding with the ACE2 receptor. Most of the theoretical studies, however, have been done on isolated proteins. ACE2 is a transmembrane protein; thus, it is important to understand the interaction of spike proteins with ACE2 in a lipid matrix. In this study, the adsorption of ACE2 and spike (N501Y) RBD at a lipid/water interface was studied using the heterodyne-detected vibrational sum frequency generation (HD-VSFG) technique. The technique is a non-linear optical spectroscopy which measures vibrational spectra of molecules at an interface and provides information on their structure and orientation. It is found that ACE2 is effectively adsorbed at the positively charged 1,2-dipalmitoyl-3-trimethylammonium-propane (DPTAP) lipid monolayer via electrostatic interactions. The adsorption of ACE2 at the DPTAP monolayer causes a reorganization of interfacial water (D2O) from the D-down to the D-up orientation, indicating that the originally positively charged DPTAP interface becomes negatively charged due to ACE2 adsorption. The negatively charged interface (DPTAP/ACE2) allows further adsorption of positively charged spike RBD. HD-VSFG spectra in the amide I region show differences for spike (N501Y) RBD adsorbed at D2O, DPTAP, and DPTAP/ACE2 interfaces. A red shift observed for the spectra of spike RBD/DPTAP suggests that spike RBD oligomers are formed upon contact with DPTAP lipids.

pH-dependent complexation of histamine H1 receptor antagonists and human serum albumin studied by UV resonance Raman spectroscopy

UV resonance Raman spectroscopy was used to characterize the binding of three first-generation histamine H(1) receptor antagonists-tripelennamine (TRP), mepyramine (MEP), and brompheniramine (BPA)-to human serum albumin (HSA) at pH 7.2 and pH 9.0. Binding constants differ at these pH values, which can be ascribed to the different extent of protonation of the ethylamino side chain of the ligands. We have recently shown [Tardioli et al. J. Raman Spectrosc. 2011, 42, 1016-1024] that for the solution conformation of TRP and MEP the side chain plays an important role by allowing an internal hydrogen bond with the aminopyridine nitrogen in TRP and MEP. Results presented in this paper suggest that the existence of such molecular structures has serious biological significance on the binding affinity of those ligands to HSA. At pH 7.2, only the stretched conformers of protonated TRP and MEP bind in HSA binding site I. Using UV absorption data, we derived binding constants for the neutral and protonated forms of TRP to HSA. The neutral species seems to be conjugated to a positive group of the protein, affecting both the tryptophan W214 and some of the tyrosine (Y) vibrations. BPA, for which the structure with an intramolecular hydrogen bonded side chain is not possible, is H bound to the indole ring nitrogen of W214, of which the side chain rotates over a certain angle to accommodate the drug in site I. We propose that the protonated BPA is also bound in site I, where the Y150 residue stabilizes the presence of this compound in the binding pocket. No spectroscopic evidence was found for conformational changes of the protein affecting the spectroscopic properties of W and Y in this pH range.

UV resonance Raman finds peptide bond-Arg side chain electronic interactions

We measured the UV resonance Raman excitation profiles and Raman depolarization ratios of the arginine (Arg) vibrations of the amino acid monomer as well as Arg in the 21-residue predominantly alanine peptide AAAAA(AAARA)(3)A (AP) between 194 and 218 nm. Excitation within the π → π* peptide bond electronic transitions result in UVRR spectra dominated by amide peptide bond vibrations. The Raman cross sections and excitation profiles indicate that the Arg side chain electronic transitions mix with the AP peptide bond electronic transitions. The Arg Raman bands in AP exhibit Raman excitation profiles similar to those of the amide bands in AP which are conformation specific. These Arg excitation profiles distinctly differ from the Arg monomer. The Raman depolarization ratios of Arg in monomeric solution are quite simple with ρ = 0.33 indicating enhancement by a single electronic transition. In contrast, we see very complex depolarization ratios of Arg in AP that indicate that the Arg residues are resonance enhanced by multiple electronic transitions.

UV resonance Raman study of TTR(105-115) structural evolution as a function of temperature

UV resonance Raman spectroscopy was used to probe the temperature dependence of the conformation of TTR(105-115) in solution. Resonance Raman spectra with excitation at 239.5 nm, show an increase in the absolute resonance Raman cross section of Tyr with an increase in temperature. This trend is associated with an increase in the hydrophobicity of the Tyr local environment, suggesting a conformational change at 28 °C. Excitation at ~200 nm is known to enhance scattering due to amide vibrations and provides insights as to the secondary structure of a peptide or protein. UVRR spectra at this excitation suggest that in solution the peptide assumes a disordered conformation with frequent formation of β-turns. Explicit-solvent replica-exchange MD simulations of the isolated peptide in the region 15 to 37 °C suggest that the dominant conformation assumed by the peptide corresponds to a coil with β-turns in the central and C-terminal region. In line with the experiments, an increase in temperature induces structural order in the peptide, reflected by an increase in the probability for the formation of β-turns and hydrophobic side-chain contacts, mainly in the 8-11 moiety, and to a lesser extent in the 4-7 moiety.

UV resonance raman investigation of electronic transitions in alpha-helical and polyproline II-like conformations

UV resonance Raman (UVRR) excitation profiles and Raman depolarization ratios were measured for a 21-residue predominantly alanine peptide, AAAAA(AAARA) 3A (AP), excited between 194 and 218 nm. Excitation within the pi-->pi* electronic transitions of the amide group results in UVRR spectra dominated by amide vibrations. The Raman cross sections and excitation profiles provide information about the nature of the electronic transitions of the alpha-helix and polyproline II (PPII)-like peptide conformations. AP is known to be predominantly alpha-helical at low temperatures and to take on a PPII helix-like conformation at high temperatures. The PPII-like and alpha-helix conformations show distinctly different Raman excitation profiles. The PPII-like conformation cross sections are approximately twice those of the alpha-helix. This is due to hypochromism that results from excitonic interactions between the NV 1 transition of one amide group with higher energy electronic transitions of other amide groups, which decreases the alpha-helical NV 1 (pi-->pi*) oscillator strengths. Excitation profiles of the alpha-helix and PPII-like conformations indicate that the highest signal-to-noise Raman spectra of alpha-helix and PPII-like conformations are obtained at excitation wavelengths of 194 and 198 nm, respectively. We also see evidence of at least two electronic transitions underlying the Raman excitation profiles of both the alpha-helical and the PPII-like conformations. In addition to the well-known approximately 190 nm pi-->pi* transitions, the Raman excitation profiles and Raman depolarization ratio measurements show features between 205-207 nm, which in the alpha-helix likely results from the parallel excitonic component. The PPII-like helix appears to also undergo excitonic splitting of its pi-->pi* transition which leads to a 207 nm feature.

Ultraviolet resonance Raman spectroscopy of folded and unfolded states of an integral membrane protein

The vibrational structure of native anchoring tryptophan (Trp) and tyrosine residues in an integral membrane protein, bacterial outer membrane protein A (OmpA), have been investigated using UV resonance Raman (UVRR) spectroscopy for the first time. Spectra of native OmpA, a single-Trp mutant, and a Trp-less mutant were recorded in folded and unfolded states, and reveal significant changes in tryptophan structure and local environment. Salient alterations upon folding include loss of hydrogen-bonding character of indole N1H, evidenced by a shift in W17 frequency from 874 and 878 cm(-1), and growth in hydrophobicity of the local tryptophan environment, supported by increase in the ratio I1361/I1340. In addition to these site-specific changes in a single tryptophan residue, modification of the vibrational structure of the remaining native tryptophan and tyrosine amino acids is also evident. Finally, the UVRR data presented here indicate that the structures of OmpA folded in vesicle and folded in detergent may differ, and provide important foundations for ongoing studies of membrane protein folding.

Interaction of angiotensin II with the C-terminal 300-320 fragment of the rat angiotensin II receptor AT1a monitored by NMR

Interaction between angiotensin II (Ang II) and the fragment peptide 300-320 (fCT300-320) of the rat angiotensin II receptor AT1a was demonstrated by relaxation measurements, NOE effects, chemical shift variations, and CD measurements. The correlation times modulating dipolar interactions for the bound and free forms of Ang II were estimated by the ratio of the nonselective and single-selective longitudinal relaxation rates. The intermolecular NOEs observed in NOESY spectra between HN protons of 9Lys(fCT) and 6His(ang), 10Phe(fCT) and 8Phe(ang), HN proton of 3Tyr(fCT) and Halpha of 4Tyr(ang), 5Phe(fCT)Hdelta and Halpha of 4Tyr(ang) indicated that Ang II aromatic residues are directly involved in the interaction, as also verified by relaxation data. Some fCT300-320 backbone features were inferred by the CSI method and CD experiments revealing that the presence of Ang II enhances the existential probability of helical conformations in the fCT fragment. Restrained molecular dynamics using the simulated annealing protocol was performed with intermolecular NOEs as constraints, imposing an alpha-helix backbone structure to fCT300-320 fragment. In the built model, one strongly preferred interaction was found that allows intermolecular stacking between aromatic rings and forces the peptide to wrap around the 6Leu side chain of the receptor fragment.

On the molecular basis of the recognition of angiotensin II (AII). NMR structure of AII in solution compared with the X-ray structure of AII bound to the mAb Fab131

The high-resolution 3D structure of the octapeptide hormone angiotensin II (AII) in aqueous solution has been obtained by simulated annealing calculations, using high-resolution NMR-derived restraints. After final refinement in explicit water, a family of 13 structures was obtained with a backbone RMSD of 0.73 +/- 0.23 A. AII adopts a fairly compact folded structure, with its C-terminus and N-terminus approaching to within approximately 7.2 A of each other. The side chains of Arg2, Tyr4, Ile5 and His6 are oriented on one side of a plane defined by the peptide backbone, and the Val3 and Pro7 are pointing in opposite directions. The stabilization of the folded conformation can be explained by the stacking of the Val3 side chain with the Pro7 ring and by a hydrophobic cluster formed by the Tyr4, Ile5 and His6 side chains. Comparison between the NMR-derived structure of AII in aqueous solution and the refined crystal structure of the complex of AII with a high-affinity mAb (Fab131) [Garcia, K.C., Ronco, P.M., Verroust, P.J., Brunger, A.T., Amzel, L.M. (1992) Science257, 502-507] provides important quantitative information on two common structural features: (a) a U-shaped structure of the Tyr4-Ile5-His6-Pro7 sequence, which is the most immunogenic epitope of the peptide, with the Asp1 side chain oriented towards the interior of the turn approaching the C-terminus; (b) an Asx-turn-like motif with the side chain aspartate carboxyl group hydrogen-bonded to the main chain NH group of Arg2. It can be concluded that small rearrangements of the epitope 4-7 in the solution structure of AII are required by a mean value of 0.76 +/- 0.03 A for structure alignment and approximately 1.27 +/- 0.02 A for sequence alignment with the X-ray structure of AII bound to the mAb Fab131. These data are interpreted in terms of a biological "nucleus" conformation of the hormone in solution, which requires a limited number of structural rearrangements for receptor-antigen recognition and binding.

Ultraviolet resonance Raman examination of horse apomyoglobin acid unfolding intermediates

We have used UV resonance Raman spectroscopy to study the acid-induced denaturation of horse apomyoglobin (apoMb) between pH 7. 0 and 1.8. The 206.5 nm excited Raman spectra are dominated by amide vibrations, which are used to quantitatively determine the apoMb secondary structure. The 229 nm excited Raman spectra are dominated by the Tyr and Trp Raman bands, which are analyzed to examine changes of Tyr and Trp environments and solvent exposures. We observe two partially unfolded apoMb intermediates at pH 4 and pH 2, while we observe only one partially unfolded holoMb intermediate at 2, in which the G and H helices are mainly intact, while the rest of protein is unfolded. This partially unfolded holoMb intermediate at pH 2 is essentially identical to the pH 2 apoMb intermediate. The partially unfolded pH 4 apoMb intermediate is composed of the three folded A, G, and H helices and contains 38% helical structure. The changes in the Trp Raman cross sections during the acid-induced denaturation indicates that Trp 7 is likely to be fully exposed in the apoMb pH 4 intermediate and that the A helix melts with a pKa approximately 3.5.

UV resonance Raman-selective amide vibrational enhancement: quantitative methodology for determining protein secondary structure

We have directly determined the amide band resonance Raman spectra of the "average" pure alpha-helix, beta-sheet, and unordered secondary structures by exciting within the amide pi-->pi* transitions at 206.5 nm. The Raman spectra are dominated by the amide bands of the peptide backbone. We have empirically determined the average pure alpha-helix, beta-sheet, and unordered resonance Raman spectra from the amide resonance Raman spectra of 13 proteins with well-known X-ray crystal structures. We demonstrate that we can simultaneously utilize the amide I, II, and III bands and the Calpha-H amide bending vibrations of these average secondary structure spectra to directly determine protein secondary structure. The UV Raman method appears to be complementary, and in some cases superior, to the existing methods, such as CD, VCD, and absorption spectroscopy. In addition, the spectra are immune to the light-scattering artifacts that plague CD, VCD, and IR absorption measurements. Thus, it will be possible to examine proteins in micelles and other scattering media.

UV resonance Raman determination of protein acid denaturation: selective unfolding of helical segments of horse myoglobin

We have used UV resonance Raman spectroscopy to study the acid denaturation of horse heart aquometmyoglobin (Mb) between pH 7.5 and 1.5. Raman spectra excited at 206.5 nm are dominated by amide vibrations, which are analyzed by using a new methodology to quantitatively determine the Mb secondary structure. In contrast, the 229-nm Raman spectra are dominated by the Tyr and Trp Raman bands, which are analyzed to examine changes in Tyr and Trp environments, such as exposure to water, hydrogen bonding, and, for Trp, any alterations of the dihedral angle between the Trp ring and its linkage to the protein backbone. We uniquely determined which Mb alpha-helices melt by combining the amide, Tyr, and Trp Raman spectral information with heme absorption spectral information. We calculate that the Mb alpha-helical composition decreases from approximately 80% at neutral pH to approximately 19% below pH 3.5. The Trp Raman cross sections dramatically decrease at low pH to values which indicate that they are fully exposed to water; this result indicates that the A helix melts. The Tyr Raman bands are pH independent, which indicates that the G and H helices around the Tyr residues do not melt. The dramatic heme absorption acid denaturation changes indicate major alterations of the heme pocket and changes in heme binding. These results indicate that the A, B, C, D, E, and F helices melt in a concerted fashion, while the antiparallel G and H helices only partially melt.