Effect of T-R conformational change on sickle-cell hemoglobin interactions and aggregation

Native Mass Spectrometry and Collision-Induced Unfolding of Laser-Ablated Proteins

Infrared laser ablation sample transfer (LAST) was used to collect samples from solid surfaces for mass spectrometry under native spray conditions. Native mass spectrometry was utilized to probe the charge states and collision-induced unfolding (CIU) characteristics of bovine serum albumin (BSA), bovine hemoglobin (BHb), and jack-bean concanavalin A (ConA) via direct injection electrospray, after liquid extraction surface sampling, and after LAST. Each protein was deposited from solution on solid surfaces and laser-ablated for off-line analysis or sampled for online analysis. It was found that the protein ion gas-phase charge-state distributions were comparable for direct infusion, liquid extraction, and laser ablation experiments. Moreover, calculated average collision cross section (CCS) values from direct injection, liquid extraction, and laser ablation experiments were consistent with previously reported literature values. Additionally, an equivalent number of mobility features and conformational turnovers were identified from unfolding pathways from all three methods for all charge states of each protein analyzed in this work. The presented work suggests that laser ablation yields intact proteins (BSA, BHb, and ConA), is compatible with native mass spectrometry, and could be suitable for spatially resolved interrogation of unfolding pathways of proteins.

The role of protein conformational switches in pharmacology: its implications in metabolic reprogramming and protein evolution

Besides pharmacogenomics and drug dynamics, pharmacological properties of a drug could also arise from protein conformational switches. These switches would arise from the following mechanisms: (a) slight shifts away from a protein's native conformation induced by mutation, (b) changes in the protein's environment allowing for structural rearrangements to form hitherto unknown conformations, (c) parsing the protein into foldable polypeptide fragment(s) by either proteolysis of the native structure or (d) perturbation of the native conformation to generate polypeptide fragment(s). These switches are modulated by changes in the protein's matrix properties such as pH, temperature, ligands-their nature, concentration and complexes; micronutrients, oxidant/antioxidant status and metabolic products within the functional environment of the protein. The pharmacological implications of these are discussed in light of polypharmacology arising from protein isomerism, cross-pharmacology, possible decreases in both the expressible and expressed protein population and metabolic reprogramming-and ultimately, how these factors relate to diseases. Further implications include variational drug toxicity and drug response idiosyncrasies. Another important consequence is that the "whole life" history of the individual would play an active role in that individual's response to disease severity and drug response up to that very moment and is prone to variations with changes in pre-disposing factors.

Dissecting the energies that stabilize sickle hemoglobin polymers

Sickle hemoglobin forms long, multistranded polymers that account for the pathophysiology of the disease. The molecules in these polymers make significant contacts along the polymer axis (i.e., axial contacts) as well as making diagonally directed contacts (i.e., lateral contacts). The axial contacts do not engage the mutant β6 Val and its nonmutant receptor region on an adjacent molecule, in contrast to the lateral contacts which do involve the mutation site. We have studied the association process by elastic light scattering measurements as a function of temperature, concentration, and primary and quaternary structure, employing an instrument of our own construction. Even well below the solubility for polymer formation, we find a difference between the association behavior of deoxy sickle hemoglobin molecules (HbS), which can polymerize at higher concentration, in comparison to COHbS, COHbA, or deoxygenated Hemoglobin A (HbA), none of which have the capacity to form polymers. The nonpolymerizable species are all quite similar to one another, and show much less association than deoxy HbS. We conclude that axial contacts are significantly weaker than the lateral ones. All the associations are entropically favored, and enthalpically disfavored, typical of hydrophobic interactions. For nonpolymerizable Hemoglobin, ΔH(o) was 35 ± 4 kcal/mol, and ΔS was 102.7 ± 0.5 cal/(mol-K). For deoxyHbS, ΔH(o) was 19 ± 2 kcal/mol, and ΔS was 56.9 ± 0.5 cal/(mol-K). The results are quantitatively consistent with the thermodynamics of polymer assembly, suggesting that the dimer contacts and polymer contacts are very similar, and they explain a previously documented significant anisotropy between bending and torsional moduli. Unexpectedly, the results also imply that a substantial fraction of the hemoglobin has associated into dimeric species at physiological conditions.

Homogeneous crystal nucleation near a metastable fluid-fluid phase transition

Several scenarios exist for the protein crystallization and aggregation in solutions near a metastable fluid-fluid phase separation below the solubility line. Based on computations, it was proposed that the fluid-fluid critical point enhances the crystallization rate by many orders of magnitude, while, based on experiments, it was proposed that the fluid-fluid spinodal controls the crystallization rate. Using molecular dynamic simulations for an isotropic model with sticky interaction, we show that neither of these scenarios adequately describes the crystallization mechanism near a metastable fluid-fluid phase separation. We find that the emergence of the high-density fluid inside the spinodal drastically enhances the crystal nucleation in the subcritical region following Ostwald's rule of stages.

Hemoglobin interactions with αB crystallin: a direct test of sensitivity to protein instability

As a small stress response protein, human αB crystallin, detects protein destabilization that can alter structure and function to cause self assembly of fibrils or aggregates in diseases of aging. The sensitivity of αB crystallin to protein instability was evaluated using wild-type hemoglobin (HbA) and hemoglobin S (HbS), the glutamate-6-valine mutant that forms elongated, filamentous aggregates in sickling red blood cells. The progressive thermal unfolding and aggregation of HbA and HbS in solution at 37°C, 50°C and 55°C was measured as increased light scattering. UV circular dichroism (UVCD) was used to evaluate conformational changes in HbA and HbS with time at the selected temperatures. The changes in interactions between αB crystallin and HbA or HbS with temperature were analyzed using differential centrifugation and SDS PAGE at 37°C, 50°C and 55°C. After only 5 minutes at the selected temperatures, differences in the aggregation or conformation of HbA and HbS were not observed, but αB crystallin bound approximately 6% and 25% more HbS than HbA at 37°C, and 50°C respectively. The results confirmed (a) the remarkable sensitivity of αB crystallin to structural instabilities at the very earliest stages of thermal unfolding and (b) an ability to distinguish the self assembling mutant form of HbS from the wild type HbA in solution.

Insights Into Crowding Effects on Protein Stability From a Coarse-Grained Model

Proteins aggregate and precipitate from high concentration solutions in a wide variety of problems of natural and technological interest. Consequently, there is a broad interest in developing new ways to model the thermodynamic and kinetic aspects of protein stability in these crowded cellular or solution environments. We use a coarse-grained modeling approach to study the effects of different crowding agents on the conformational equilibria of proteins and the thermodynamic phase behavior of their solutions. At low to moderate protein concentrations, we find that crowding species can either stabilize or destabilize the native state, depending on the strength of their attractive interaction with the proteins. At high protein concentrations, crowders tend to stabilize the native state due to excluded volume effects, irrespective of the strength of the crowder-protein attraction. Crowding agents reduce the tendency of protein solutions to undergo a liquid-liquid phase separation driven by strong protein-protein attractions. The aforementioned equilibrium trends represent, to our knowledge, the first simulation predictions for how the properties of crowding species impact the global thermodynamic stability of proteins and their solutions.

Early stages of beta2-microglobulin aggregation and the inhibiting action of alphaB-crystallin

Static and dynamic light scattering experiments on extremely clean (nanofiltered) samples of the well-known amyloidogenic protein beta2-microglobulin (R3Abeta2m and WTbeta2m) evidence the self-assembly of early aggregates showing unexpected features. Further, we find that alphaB-crystallin effectively inhibits aggregation of beta2m in a far less than stoichiometric proportion, from 1:60 alphaB-crystallin monomer to beta2m monomer ratio, down to at least a 1:2 x 10(3) alphaB-crystallin oligomerto beta2m monomer ratio. Therefore, inhibition of the early stage of beta2m aggregation by alphaB-crystallin does not necessarily require a mechanicistic chaperon-like action implying one-to-one binding. This highlights the role of the free energy landscape of the system and of related modifications of solute-solvent thermodynamics caused by co-solutes, in agreement with recent work from our and other laboratories.

The Effect of a Point Mutation on the Stability of IgG4 as Monitored by Analytical Ultracentrifugation

There is presently considerable interest in the state of aggregation and biophysical integrity of antibody preparations, and recent advances in the analysis of data from the analytical ultracentrifuge renders it a powerful probe of these stability phenomena, under both storage and freeze-thaw conditions. Solutions of a wild-type IgG4 antibody and a single amino acid hinge mutant IgG4m (serine residue 241 converted to proline) were exposed to different accelerated stress conditions, namely (i) elevated temperature storage for various periods (up to 59 days at 37 degrees C) or (ii) a series of freeze-thaw cycles (storage at -80 degrees C then incubation at 20 degrees C for 1 h under different conditions). Analysis using the nondisruptive probe of sedimentation velocity in the analytical ultracentrifuge indicated that for both antibodies the monomer was always the most common species present whatever storage regime had been used. Sedimentation coefficient distribution analysis showed that other higher oligomer species and half-antibodies were present, and appeared to be not in chemical equilibrium with each other. Solution heterogeneity was found to increase considerably with treatment for both native and hinge-mutant antibodies although the latter appeared to be more resistant to freeze-thaw-induced aggregation.

Protein aggregation/crystallization and minor structural changes: universal versus specific aspects

Protein association covers wide interests in biophysics, protein science, and biotechnologies, and it is often viewed as governed by conformation details. More recently, the existence of a universal physical principle governing aggregation/crystallization processes has been suggested by a series of experiments and shown to be linked to the universal scaling properties of concentration fluctuations occurring in the proximity of a phase transition (spinodal demixing in the specific case). Such properties have provided a quantitative basis for capturing kinetic association data on a universal master curve, ruled by the normalized distance of the state of the system from its instability region. Here we report new data on lysozyme crystal nucleation. They strengthen the evidence in favor of universality and show that the system enters the region of universal behavior in a stepwise manner as a result of minor conformation changes. Results also show that the link between conformation details and universal behavior is actuated by interactions mediated by the solvent. Outside the region of universal behavior, nucleation rates become unpredictable and undetectably long.

Coarse-grained strategy for modeling protein stability in concentrated solutions. III: directional protein interactions

We extend our coarse-grained modeling strategy described in parts I and II of this investigation to account for nonuniform spatial distributions of hydrophobic residues on the solvent-exposed surfaces of native proteins. Within this framework, we explore how patchy surfaces can influence the solvent-mediated protein-protein interactions, and the unfolding and self-assembly behaviors of proteins in solution. In particular, we compare the equilibrium unfolding and self-assembly trends for three model proteins that share the same overall sequence hydrophobicity, but exhibit folded configurations with different solvent-exposed native-state surface morphologies. Our model provides new insights into how directional interactions can affect native-state protein stability in solution. We find that strongly-directional attractions between native molecules with patchy surfaces can help stabilize the folded conformation through the formation of self-assembled clusters. In contrast, native proteins with more uniform surfaces are destabilized by protein-protein attractions involving the denatured state. Finally, we discuss how the simulation results provide insights into the experimental solution behaviors of several proteins that display directional interactions in their native states.

Coarse-grained strategy for modeling protein stability in concentrated solutions. II: phase behavior

We use highly efficient transition-matrix Monte Carlo simulations to determine equilibrium unfolding curves and fluid phase boundaries for solutions of coarse-grained globular proteins. The model we analyze derives the intrinsic stability of the native state and protein-protein interactions from basic information about protein sequence using heteropolymer collapse theory. It predicts that solutions of low hydrophobicity proteins generally exhibit a single liquid phase near their midpoint temperatures for unfolding, while solutions of proteins with high sequence hydrophobicity display the type of temperature-inverted, liquid-liquid transition associated with aggregation processes of proteins and other amphiphilic molecules. The phase transition occurring in solutions of the most hydrophobic protein we study extends below the unfolding curve, creating an immiscibility gap between a dilute, mostly native phase and a concentrated, mostly denatured phase. The results are qualitatively consistent with the solution behavior of hemoglobin (HbA) and its sickle variant (HbS), and they suggest that a liquid-liquid transition resulting in significant protein denaturation should generally be expected on the phase diagram of high-hydrophobicity protein solutions. The concentration fluctuations associated with this transition could be a driving force for the nonnative aggregation that can occur below the midpoint temperature.