Abstract:The mechanism of protein–polyelectrolyte
complexation on
the wrong side of the isoelectric point has long puzzled researchers.
Two alternative explanations have been proposed in the literature:
(a) the charge-patch (CP) mechanism, based on the inhomogeneous distribution
of charges on the protein, and (b) the charge-regulation (CR) mechanism,
based on the variable charge of weak acid and base groups, which may
invert the protein charge in the presence of another highly charged
object. To discern these two mecha… Show more
“…In doing so, the electrostatic interactions are fully described by this simple and robust model. The charge regulation mechanism that can result in additional mesoscopic attractive electrostatic forces 68,69,91 is properly incorporated. Non-titratable amino acids are kept neutral all the time.…”
Section: Molecular Systems and Their Modelingmentioning
confidence: 99%
“…Here, pH is an input parameter as is the temperature). 66 This implies that possible contributions from mesoscopic electrostatic mechanisms as the charge regulation phenomena due to the proton fluctuations [67][68][69] were not considered and/or quantified in many previous works. Similarly, calculations were performed almost exclusively at pH 7.…”
Electrostatic intermolecular interactions are important in many aspects of biology. We have studied the main electrostatic features involved in the interaction of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with the human receptor Angiotensin-converting enzyme 2 (ACE2). As the principal computational tool, we have used the FORTE approach, capable to model proton fluctuations and computing free energies for a very large number of protein-protein systems under different physical-chemical conditions, here focusing on the RBD-ACE2 interactions. Both the wild-type and all critical variants are included in this study. From our large ensemble of extensive simulations, we obtain, as a function of pH, the binding affinities, charges of the proteins, their charge regulation capacities, and their dipole moments. In addition, we have calculated the pKas for all ionizable residues and mapped the electrostatic coupling between them. We are able to present a simple predictor for the RBD-ACE2 binding based on the data obtained for Alpha, Beta, Gamma, Delta, and Omicron variants, as a linear correlation between the total charge of the RBD and the corresponding binding affinity. This RBD charge rule should work as a quick test of the degree of severity of the coming SARS-CoV-2 variants in the future.
“…In doing so, the electrostatic interactions are fully described by this simple and robust model. The charge regulation mechanism that can result in additional mesoscopic attractive electrostatic forces 68,69,91 is properly incorporated. Non-titratable amino acids are kept neutral all the time.…”
Section: Molecular Systems and Their Modelingmentioning
confidence: 99%
“…Here, pH is an input parameter as is the temperature). 66 This implies that possible contributions from mesoscopic electrostatic mechanisms as the charge regulation phenomena due to the proton fluctuations [67][68][69] were not considered and/or quantified in many previous works. Similarly, calculations were performed almost exclusively at pH 7.…”
Electrostatic intermolecular interactions are important in many aspects of biology. We have studied the main electrostatic features involved in the interaction of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with the human receptor Angiotensin-converting enzyme 2 (ACE2). As the principal computational tool, we have used the FORTE approach, capable to model proton fluctuations and computing free energies for a very large number of protein-protein systems under different physical-chemical conditions, here focusing on the RBD-ACE2 interactions. Both the wild-type and all critical variants are included in this study. From our large ensemble of extensive simulations, we obtain, as a function of pH, the binding affinities, charges of the proteins, their charge regulation capacities, and their dipole moments. In addition, we have calculated the pKas for all ionizable residues and mapped the electrostatic coupling between them. We are able to present a simple predictor for the RBD-ACE2 binding based on the data obtained for Alpha, Beta, Gamma, Delta, and Omicron variants, as a linear correlation between the total charge of the RBD and the corresponding binding affinity. This RBD charge rule should work as a quick test of the degree of severity of the coming SARS-CoV-2 variants in the future.
“…At pHs conditions closer to 7, NS1 ZIKV-UG and NS1 ZIKV-BR in the dimeric states have a particular characteristic presenting higher dipole values than the remaining NS1 flavivirus . These observations indicate that charge regulation and dipole interactions (Barroso da Silva et al, 2006; Da Silva and Jönsson, 2009; Lunkad et al, 2022) can play a more important and specific role for each viral system when the salt concentration is sufficiently low.…”
Section: Resultsmentioning
confidence: 90%
“…Only titration was included as an MC movement in these runs. The FPTS was employed at a different pH condition from 0.1 to 14 every 0.1 pH unit to compute the corresponding protein net charge number ( Z P ), the charge regulation capacity ( C P ), and the dipole moment number ( μ P ) as previously proposed (Delboni and Da Silva, 2016; Jonsson and Lund, 2007; Lunkad et al, 2022; Poveda-Cuevas et al, 2018). For the other simulation sets where the focus was on the complexation process, much longer and quite expensive (in terms of CPU time) simulations were necessary.…”
Flaviviruses comprise a large group of arboviral species that are distributed in several countries of the tropics, neotropics, and some temperate zones. Since they can produce neurological pathologies or vascular damage, there has been intense research seeking better diagnosis and treatments for their infections in the last decades. The flavivirus NS1 protein is a relevant clinical target because it is involved in viral replication, immune evasion, and virulence. Being a key factor in endothelial and tissue-specific modulation, NS1 has been largely studied to understand the molecular mechanisms exploited by the virus to reprogram host cells. A central part of the viral maturation processes is the NS1 oligomerization because many stages rely on these protein-protein assemblies. In the present study, the self-associations of NS1 proteins from Zika, Dengue, and West Nile viruses are examined through constant-pH coarse-grained biophysical simulations. Free energies of interactions were estimated for different oligomeric states and pH conditions. Our results show that these proteins can form both dimers and tetramers under conditions near physiological pH even without the presence of lipids. Moreover, pH plays an important role mainly controlling the regimes where van der Waals interactions govern their association. Finally, despite the similarity at the sequence level, we found that each flavivirus has a well-characteristic protein-protein interaction profile. These specific features can provide new hints for the development of binders both for better diagnostic tools and the formulation of new therapeutic drugs.
“…An alternative mechanism to the charge-patch mechanism used in the literature to explain the complexation on the "wrong side" is the so-called charge-regulation mechanism. Although the two mechanisms (charge-patch and charge-regulation) are not mutually exclusive, as recently shown by Lunkand et al, 62 the ability of BSA to chargeregulate at pH ≈ 8.0 is low. 25 In addition, charge regulation is usually considered at low ionic strengths (a few mM), and bearing in mind that we performed our measurements at larger ionic strengths (I total = 20 mM), the association between NaPSS and BSA at pH = 8.0, where BSA also has a large dipole moment, 63,64 is most likely a consequence of the charge-patch mechanism.…”
In the protein purification, drug delivery, food industry, and biotechnological applications involving protein−polyelectrolyte complexation, proper selection of co-solutes and solution conditions plays a crucial role. The onset of (bio)macromolecular complexation occurs even on the so-called "wrong side" of the protein isoionic point where both the protein and the polyelectrolyte are net like-charged. To gain mechanistic insights into the modulatory role of salts (NaCl, NaBr, and NaI) and sugars (sucrose and sucralose) in protein− polyelectrolyte complexation under such conditions, interaction between bovine serum albumin (BSA) and sodium polystyrene sulfonate (NaPSS) at pH = 8.0 was studied by a combination of isothermal titration calorimetry, fluorescence spectroscopy, circular dichroism, and thermodynamic modeling. The BSA−NaPSS complexation proceeds by two binding processes (first, formation of intrapolymer complexes and then formation of interpolymer complexes), both driven by favorable electrostatic interactions between the negatively charged sulfonic groups (−SO 3 − ) of NaPSS and positively charged patches on the BSA surface. Two such positive patches were identified, each responsible for one of the two binding processes. The presence of salts screened both short-range attractive and long-range repulsive electrostatic interactions between both macromolecules, resulting in a nonmonotonic dependence of the binding affinity on the total ionic strength for both binding processes. In addition, distinct anion-specific effects were observed (NaCl < NaBr < NaI). The effect of sugars was less pronounced: sucrose had no effect on the complexation, but its chlorinated analogue, sucralose, promoted it slightly due to the screening of long-range repulsive electrostatic interactions between BSA and NaPSS. Although short-range nonelectrostatic interactions are frequently mentioned in the literature in relation to BSA or NaPSS, we found that the main driving force of complexation on the "wrong side" are electrostatic interactions.
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