Multi-state Binding Research Articles

Deciphering the multi-state binding and dissociation of fenofibrate with β-cyclodextrin and its derivatives: Insights from phase solubility analysis and molecular modeling

The present study focuses on elucidating the multi-state binding and dissociation interaction of fenofibrate (FNB) with β-cyclodextrin and its derivatives hydroxypropyl-β-cyclodextrin (HP-β-CD) and sulfobutylether-β-cyclodextrin (SBE-β-CD), with a specific emphasis on the correlation between phase solubility analysis and molecular modeling. The dynamic complexation, conformational stability, configuration transition, and binding energy (ΔEbinding) were investigated based on molecular dynamics (MD) simulations. Subsequently, the quantum mechanical calculations were performed to strengthen the MD results. The dissociation of FNB from both rims of the three cyclodextrins (CDs) was examined using umbrella sampling simulations. The FNB molecule was found to bind to CD in a 1:1 stoichiometry with spontaneous and thermodynamic favorability. The binding ability of FNB with three CDs was arranged in the following sequence: SBE-β-CD > HP-β-CD > β-CD. Moreover, the binding conformations in parallel showed a lower ΔEbinding than those in an anti-parallel arrangement. The FNB molecule exhibited an equal probability of dissociating from the primary and secondary cavity orientations of β-CD. In contrast, for HP-β-CD and SBE-β-CD, FNB tended to dissociate from the primary cavity positions. The combination of the phase solubility method with molecular modeling afforded an in-depth and comprehensive understanding of the interactions between FNB and different CDs and has the potential to be generally applicable to the design and optimization of CD carrier materials to enhance the water solubility of poorly soluble compounds.

Lactadherin's Multistate Binding Predicts Stable Membrane-Bound Conformations of Factors V and VIII's C Domains.

Protein binding to negatively charged lipids is essential for maintaining numerous vital cellular processes where its dysfunction can lead to various diseases. One such protein that plays a crucial role in this process is lactadherin, which competes with coagulation factors for membrane binding sites to regulate blood clotting. Despite identifying key binding regions of these proteins through structural and biochemical studies, models incorporating membrane dynamics are still lacking. In this study, we report on the multimodal binding of lactadherin and use it to gain insight into the binding mechanisms of its C domain homologs, factor V and factor VIII. Molecular dynamics simulations enhanced with the highly mobile mimetic model enabled the determination of lactadherin's multimodal binding on membranes that revealed critical interacting residues consistent with prior NMR and mutagenesis data. The binding occurred primarily via two dynamic structural ensembles: an inserted state and an unreported, highly conserved side-lying state driven by a cationic patch. We utilized these findings to analyze the membrane binding domains of coagulation factors V and VIII and identified their preferred membrane-bound conformations. Specifically, factor V's C domains maintained an inserted state, while factor VIII preferred a tilted, side-lying state that permitted antibody binding. Insight into lactadherin's atomistically resolved membrane interactions from a multistate perspective can guide new therapeutic opportunities in treating diseases related to blood coagulation.

Quantitative Multistate Binding Model of Silica Nanoparticle-Protein Interactions Obtained from Multinuclear Spin Relaxation.

Nanoparticle-assisted NMR spin relaxation (NASR), which makes internal protein dynamics in solution directly observable on nanosecond to microsecond time scales, has been applied to different nuclei and relaxation processes of the same protein system. A model is presented describing the transient interaction between ubiquitin and anionic silica nanoparticles for the unified interpretation of a wealth of experimental data including 2H, 13C, and 15N relaxation of methyl side chain and backbone moieties. The best model, implemented using a stochastic Liouville equation, describes the exchange process via an intermediary encounter state between free and fully nanoparticle-bound protein. The implication of the three-state binding model on the interpretation of NASR data is discussed.

Molecular dynamics simulations of the conformational plasticity in the active pocket of salt-inducible kinase 2 (SIK2) multi-state binding with bosutinib

The kinase domain is highly conserved among protein kinases 'in terms of both sequence and structure. Conformational rearrangements of the kinase domain are affected by the phosphorylation of residues and the binding of kinase inhibitors. Interestingly, the conformational rearrangement of the active pocket plays an important role in kinase activity and can be used to design novel kinase inhibitors. We characterized the conformational plasticity of the active pocket when bosutinib was bound to salt-inducible kinase 2 (SIK2) using homology modeling and molecular dynamics simulations. Ten different initial complex models were constructed using the Morph server, ranging from open to closed conformations of SIK2 binding with bosutinib. Our simulation showed that bosutinib binds SIK2 with up or down conformations of the P-loop and with all the conformations of the activation loop. In addition, the αC-helix conformation was induced by the conformation of the activation loop, and the salt bridge formed only with its open conformation. The binding affinity of the models was also determined using the molecular mechanics generalized Born surface area method. Bosutinib was found to form a strong binding model with SIK2 and hydrophobic interactions were the dominant factor. This discovery may help guide the design of novel SIK2 inhibitors.

Multi-state recognition pathway of the intrinsically disordered protein kinase inhibitor by protein kinase A.

In the nucleus, the spatiotemporal regulation of the catalytic subunit of cAMP-dependent protein kinase A (PKA-C) is orchestrated by an intrinsically disordered protein kinase inhibitor, PKI, which recruits the CRM1/RanGTP nuclear exporting complex. How the PKA-C/PKI complex assembles and recognizes CRM1/RanGTP is not well understood. Using NMR, SAXS, fluorescence, metadynamics, and Markov model analysis, we determined the multi-state recognition pathway for PKI. After a fast binding step in which PKA-C selects PKI's most competent conformations, PKI folds upon binding through a slow conformational rearrangement within the enzyme's binding pocket. The high-affinity and pseudo-substrate regions of PKI become more structured and the transient interactions with the kinase augment the helical content of the nuclear export sequence, which is then poised to recruit the CRM1/RanGTP complex for nuclear translocation. The multistate binding mechanism featured by PKA-C/PKI complex represents a paradigm on how disordered, ancillary proteins (or protein domains) are able to operate multiple functions such as inhibiting the kinase while recruiting other regulatory proteins for nuclear export.

Multi-state steric mass action model and case study on complex high loading behavior of mAb on ion exchange tentacle resin

Tentacle resins for IEX are increasingly applied in preparative chromatography for their higher selectivity and higher capacities in comparison to IEX resins without tentacles. However, tentacle resins are often observed to cause unusual elution behavior of monoclonal antibodies under high loading conditions. Understanding this elution behavior is important for a quality by design approach, as it is now mandated by regulatory agencies. A model-based analysis of load, wash and gradient elution is performed for a monoclonal antibody (mAb) on Fractogel SO3−. Four experiments with increasing loaded mass show complex peak shapes and formation of a shoulder under overloaded conditions. We hypothesize that the observed peak shapes are caused by mAbs binding in multiple states on the tentacle ion-exchange resin. A new multi-state SMA binding model is used for testing this hypothesis. A two-state binding model is found to quantitatively reproduce all four experiments. An in-depth analysis reveals that the shoulder formation under overloaded conditions can be explained by multi-state binding that particularly manifests in rapid but weak re-adsorption of eluting molecules near the column end. The introduced multi-state SMA model combines features of the so-called spreading model (multiple bound states) and of the standard SMA model (salt dependency). It is by no means limited to ion-exchange chromatography on tentacle resins, but the same concept can be applied for studying systems that are based on other physical mechanisms. The new model can potentially improve mechanistic understanding and facilitate quantitative simulation of various phenomena, such as caused by reorientation, reconformation or unfolding of bound species. Similar concepts can be applied for studying surface-induced aggregation and denaturation.

NMR line shapes and multi-state binding equilibria

Biological function of proteins relies on conformational transitions and binding of specific ligands. Protein-ligand interactions are thermodynamically and kinetically coupled to conformational changes in protein structures as conceptualized by the models of pre-existing equilibria and induced fit. NMR spectroscopy is particularly sensitive to complex ligand-binding modes-NMR line-shape analysis can provide for thermodynamic and kinetic constants of ligand-binding equilibria with the site-specific resolution. However, broad use of line shape analysis is hampered by complexity of NMR line shapes in multi-state systems. To facilitate interpretation of such spectral patterns, I computationally explored systems where isomerization or dimerization of a protein (receptor) molecule is coupled to binding of a ligand. Through an extensive analysis of multiple exchange regimes for a family of three-state models, I identified signature features to guide an NMR experimentalist in recognizing specific interaction mechanisms. Results show that distinct multi-state models may produce very similar spectral patterns. I also discussed aggregation of a receptor as a possible source of spurious three-state line shapes and provided specific suggestions for complementary experiments that can ensure reliable mechanistic insight.

Mechanism of Action of the Photoswitch Molecule QAQ

Controlling neuronal excitability with light has emerged as a powerful and widely used approach in Neuroscience. Optogenetic tools function by enabling light to activate exogenously expressed ion channels that over-power endogenous electrophysiogical processes.In contrast, we have introduced a non-genetic approach to conferring light sensitivity on neurons that involves photochemical tools that regulate endogenous ion channels. Specifically, the design of the molecule QAQ is built around an azobenzene photoswitch group flanked by two symmetric quaternary ammonium groups which confer the ability to intracellularly block voltage-gated sodium, potassium and calcium channels. Blocking can be regulated by rapid and reversible photoisomerization of the central azobenzene group from trans to cis configuration upon 380 or 500nm light illumination, respectively. QAQ in its trans configuration blocks ion conduction through open channels enabling light-sensitive silencing of neurons while conversion to the cis configuration relieves the block.Given its double-charged character, QAQ is membrane-impermeable but it can enter cells through TRPV1 or P2X7 receptors if they are active. Since TRPV1 is mainly expressed in dorsal root ganglia neurons and participates in the perception of various external stimuli and pain, QAQ functions as a local anesthetic inhibiting neuronal excitibitly after cell entry.In that context, we have demonstrated that QAQ can modify nociception after selective loading of active pain neurons. However, the precise biophysical mechanism of action of QAQ on voltage-gated channels remains unclear. Therefore, we conducted an extended biophysical characterization using excised inside-out patches to elucidate binding characteristics of both QAQ configurations on a reporter channel, the voltage-gated potassium channel Shaker. Experiments involving mutations of Shaker and monitoring of QAQ trapping upon gate closure revealed interactions of QAQ with the channel. In summary, we examined the state-dependent persistence of blocking and our findings lead to multi-state binding model.

Lifetime Measurements Reveal Kinetic Differences between Homophilic Cadherin Bonds

Cadherins are multidomain adhesion proteins whose interactions direct cell sorting during histogenesis. They determine cell adhesion specificity, but prior studies failed to identify physical differences that could underlie cell sorting. These single molecule studies identify kinetic and strength differences between different cadherins. They further demonstrate that the modular extracellular architecture of cleavage stage C-cadherin supports a multistate binding mechanism. These multiple bonds exhibit a kinetic hierarchy of strengths that map to the different cadherin domains. The outer two N-terminal domains of C-cadherin form two bound states with dissociation rates of 3.9 and 0.02 s −1. The latter is 25-fold slower than between the corresponding epithelial cadherin segments. In addition to the two fast bonds, the five-domain fragment (CEC1-5) forms two additional stronger, longer-lived bonds with dissociation rates of 0.00039 and 0.00001 s −1. We further quantified the lifetimes of bonds subject to a constant force, and thus identified multiple dissociation events with rates that agree quantitatively with the force spectroscopy data. The qualitative features are similar to those reported for epithelial cadherin. However, the significant differences in the dissociation rates of the outer domains, which include the specificity-determining region, suggest that kinetic differences may determine cadherin discrimination, rather than adhesion energies.

Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate.

We report the 1.96 A crystal structure of pyridoxine 5'-phosphate synthase (PdxJ) in complex with 1-deoxy-D-xylulose phosphate (dXP). The octameric enzyme possesses eight distinct binding sites, and three different binding states are observed. The observation of these three states supports a mechanism in which precise conformational changes of a peptide loop and groups of active site residues modulate binding and specificity. The differences in protein conformation when one or two substrates are bound can be correlated with a condensation mechanism that leads productively to the formation of pyridoxine 5'-phosphate (PNP). "Snapshots" of the progression from the apo form to a singly occupied "transitional binding" state and, subsequently, to a fully occupied, reactive state are revealed and indicate how the enzyme structure can be related to a plausible catalytic mechanism and, moreover, to favorable energetics of reaction.