Core-shell model of the clusters of CPEB4 isoforms preceding liquid-liquid phase separation.

Protein solutions can undergo liquid-liquid phase separation (LLPS), where a dispersed phase with a low protein concentration coexists with coacervates with a high protein concentration. We focus on the low complexity N-terminal domain of cytoplasmic polyadenylation element binding-4 protein, CPEB4NTD, and its isoform depleted of the Exon4, CPEB4Δ4NTD. They both exhibit LLPS, but in contrast to most systems undergoing LLPS, the single-phase regime preceding LLPS consists mainly of soluble protein clusters. We combine experimental and theoretical approaches to resolve the internal structure of the clusters and the basis for their formation. Dynamic light scattering (DLS) and atomic force microscopy (AFM) show that both isoforms exhibit clusters with diameters ranging from 35-80 nm. Electron paramagnetic resonance (EPR) spectroscopy of spin-labeled CPEB4NTD and CPEB4Δ4NTD revealed that these proteins have two distinct dynamical properties in the clusters and coacervates. Based on the experimental results, we proposed a core-shell structure for the clusters, which is supported by the agreement of the DLS data on cluster size distribution with a statistical model developed to describe the structure of clusters. This model treats clusters as swollen micelles (microemulsions) where the core and the shell regions comprise different protein conformations, in agreement with the EPR detection of two protein populations. The effects of ionic strength and the addition of 1,6-hexanediol (HD) were used to probe the interactions responsible for cluster formation. While both CPEB4NTD and CPEB4Δ4NTD showed phase separation with increasing temperature and formed clusters, differences were found in the properties of the clusters and the coacervates. The data also suggested that the coacervates may consist of aggregates of clusters.

DEER experiments reveal fundamental differences between calmodulin complexes with IQ and MARCKS peptides in solution.

Calmodulin (CaM) is a calcium-binding protein that regulates the function of many proteins by indirectly conferring Ca2+ sensitivity, and it undergoes a large conformational change on partners' binding. We compared the solution binding mode of the target peptides MARCKS and IQ by double electron-electron resonance (DEER) distance measurements and paramagnetic NMR. We combined nitroxide and Gd(III) spin labels, including specific substitution of one of the Ca2+ ions in the CaM mutant N60D by a Gd(III) ion. The binding of MARCKS to holo-CaM resulted neither in a closed conformation nor in a unique relative orientation between the two CaM domains, in contrast with the crystal structure. Binding of IQ to holo-CaM did generate a closed conformation. Using elastic network modeling and 12 distance restraints obtained from multiple holo-CaM/IQ DEER data, we derived a model of the solution structure, which is in reasonable agreement with the crystal structure.

Evolution of CPEB4 Dynamics Across its Liquid-Liquid Phase Separation Transition.

Knowledge about the structural and dynamic properties of proteins that form membrane-less organelles in cells via liquid-liquid phase separation (LLPS) is required for understanding the process at a molecular level. We used spin labeling and electron paramagnetic resonance (EPR) spectroscopy to investigate the dynamic properties (rotational diffusion) of the low complexity N-terminal domain of cytoplasmic polyadenylation element binding-4 protein (CPEB4NTD) across its LLPS transition, which takes place with increasing temperature. We report the coexistence of three spin labeled CPEB4NTD (CPEB4*) populations with distinct dynamic properties representing different conformational spaces, both before and within the LLPS state. Monomeric CPEB4* exhibiting fast motion defines population I and shows low abundance prior to and following LLPS. Populations II and III are part of CPEB4* assemblies where II corresponds to loose conformations with intermediate range motions and population III represents compact conformations with strongly attenuated motions. As the temperature increased the population of component II increased reversibly at the expense of component III, indicating the existence of an III ⇌ II equilibrium. We correlated the macroscopic LLPS properties with the III ⇌ II exchange process upon varying temperature and CPEB4* and salt concentrations. We hypothesized that weak transient intermolecular interactions facilitated by component II lead to LLPS, with the small assemblies integrated within the droplets. The LLPS transition, however, was not associated with a clear discontinuity in the correlation times and populations of the three components. Importantly, CPEB4NTD exhibits LLPS properties where droplet formation occurs from a preformed microscopic assembly rather than the monomeric protein molecules.

Polyamines and its analogue modulates amyloid fibrillation in lysozyme: A comparative investigation.

BACKGROUND: Polyamines can induce protein aggregation that can be related to the physiology of the cellular function. Polyamines have been implicated in protein aggregation which may lead to neuropathic and non neuropathic amyloidosis. SCOPE OF REVIEW: Change in the level of polyamine concentration has been associated with ageing and neurodegeneration such as Parkinson's disease, Alzheimer's disease. Lysozyme aggregation in the presence of polyamines leads to non neuropathic amyloidosis. Polyamine analogues can suppress or inhibit protein aggregation suggesting their efficacy against amyloidogenic protein aggregates. MAJOR CONCLUSIONS: In this study we report the comparative interactions of lysozyme with the polyamine analogue, 1-naphthyl acetyl spermine in comparison with the biogenic polyamines through spectroscopy, calorimetry, imaging and docking techniques. The findings revealed that the affinity of binding varied as spermidine > 1-naphthyl acetyl spermine > spermine. The biogenic polyamines accelerated the rate of fibrillation significantly, whereas the analogue inhibited the rate of fibrillation to a considerable extent. The polyamines bind near the catalytic diad residues viz. Glu35 and Asp52, and in close proximity of Trp62 residue. However, the analogue showed dual nature of interaction where its alkyl amine region bind in same way as the biogenic polyamines bind to the catalytic site, while the naphthyl group makes hydrophobic contacts with Trp62 and Trp63, thereby suggesting its direct influence on fibrillation. GENERAL SIGNIFICANCE: This study, thus, potentiates, the development of a polyamine analogue that can perform as an effective inhibitor targeted towards aggregation of amyloidogenic proteins.

Chelerythrine-lysozyme interaction: spectroscopic studies, thermodynamics and molecular modeling exploration.

The binding of the iminium and alkanolamine forms of chelerythrine to lysozyme (Lyz) was investigated by spectroscopy and docking studies. The thermodynamics of the binding was studied by calorimetry. Spectroscopic evidence suggested that Trp-62 and Trp-63 in the ß-domain of the protein are closer to the binding site; moreover, the binding site was at a distance of 2.27 and 2.00 nm from the iminium and alkanolamine forms, respectively, according to the Forster theory of non-radiation energy transfer. The equilibrium binding constants for the iminium and alkanolamine forms at 298 K were evaluated to be 1.29 × 10(5) and 7.79 × 10(5) M(-1), respectively. The binding resulted in an alteration of the secondary structure of the protein with a distinct reduction of the helical organization. The binding of iminium was endothermic, involving electrostatic and hydrophobic interactions, while that of alkanolamine form was exothermic and dominated by hydrogen bonding interactions. Docking studies provided the atomistic details pertaining to the binding of both forms of chelerythrine and supported the higher binding in favour of the alkanolamine over the iminium. Furthermore, molecular dynamics study provided accurate insights regarding the binding of both chelerythrine forms in accordance with the experimental results obtained. Chelerythrine binding pocket involves the catalytic region and aggregation prone K-peptide region, which are sandwiched between one another. Overall, these results suggest that both the forms of the alkaloid bind to the protein but the neutral form has higher affinity than the cationic form.

Binding of the iminium and alkanolamine forms of sanguinarine to lysozyme: spectroscopic analysis, thermodynamics, and molecular modeling studies.

Sanguinarine (SGR) exists in charged iminium (SGRI) and neutral alkanolamine (SGRA) forms. The binding of these two forms to the protein lysozyme (Lyz) was investigated by fluorescence, UV-vis absorbance and circular dichroism spectroscopy, and in silico molecular docking approaches. Binding thermodynamics were studied by microcalorimetry. Both forms of sanguinarine quenched the intrinsic fluorescence of Lyz, but the quenching efficiencies varied on the basis of binding that was derived after correction for an inner-filter effect. The equilibrium binding constants at 25 ± 1.0 °C for the iminium and alkanolamine forms were 1.17 × 10(5) and 3.32 × 10(5) M(-1), respectively, with approximately one binding site for both forms of the protein. Conformational changes of the protein in the presence of SGR were confirmed by absorbance, circular dichroism, three-dimensional fluorescence, and synchronous fluorescence spectroscopy. Microcalorimetry data revealed that SGRI binding is endothermic and predominantly involves electrostatic and hydrophobic interactions, whereas SGRA binding is exothermic and dominated by hydrogen-bonding interactions. The molecular distances (r) of 3.27 and 3.04 nm between the donor (Lyz) and the SGRI and SGRA acceptors, respectively, were calculated according to Förster's theory. These data suggested that both forms were bound near the Trp-62/63 residues of Lyz. Stronger binding of SGRA than SGRI was apparent from the results of both structural and thermodynamic experiments. Molecular docking studies revealed that the putative binding site for the SGR analogues resides at the catalytic site. The docking results are in accordance with the spectroscopic and thermodynamic data, further validating the stronger binding of SGRA over SGRI to Lyz. The binding site is situated near a deep crevice on the protein surface and is close to several crucial amino acid residues, including Asp-52, Glu-35, Trp-62, and Trp-63. This study advances our knowledge of the structural nature and thermodynamic aspects of binding between the putative anticancer alkaloid sanguinarine and lysozyme.

Protein unfolding and subsequent refolding: a spectroscopic investigation.

The mechanism by which the protein Bovine Serum Albumin (BSA) undergoes unfolding induced by Guanidine Hydrochloride (GdHCl) and then the subsequent refolding brought in by many-fold dilution was studied by steady-state fluorescence, anisotropy, time resolved measurements and Circular Dichroism (CD) spectroscopy. CD data reveal that the protein attains a degree of extra rigidity at low concentrations of the denaturant, GdHCl, and this observation was correlated with other techniques used in this present work. The unfolding and refolding of BSA appear to proceed through intermediates and both the processes are sequential in nature. The intrinsic fluorescence from the tryptophan amino acid residue of BSA and another external fluorophore Nile Red was made use of in order to investigate the mechanisms of unfolding and refolding and we have conclusively proved that both these processes follow a reversible mechanism.

Spectroscopic determination of Critical Micelle Concentration in aqueous and non-aqueous media using a non-invasive method.

In this present study, we report on new methodology for determining the Critical Micelle Concentration (CMC) of a neutral surfactant Triton X-100 (TX-100) both in aqueous and non-aqueous media based on a non-invasive approach. The presence of the phenyl moiety of TX-100 was made use of as an intrinsic fluorophore and steady-state and time-resolved spectroscopy has been used to characterize the micellar systems. There are reports that external fluorophores may bring about some structural changes in the systems and the perturbations caused by these fluorophores in micellar systems may affect the shape and size of the micelles. We have also used three probes namely ANS, Rh6G and C-480 to determine the CMC of TX-100 both in aqueous and non-aqueous media and the values obtained agree very well with those estimated by the non-invasive techniques. Interestingly, for our system, we have conclusively proved that the external probes have almost no effect on the process of micellization. Although, both the invasive and non-invasive technologies report almost the same values of CMC, yet the latter methodology is free from any external perturbations and this makes the micellar/reverse micellar system, which may interact with other biological systems less prone to any physical distortions.

Exploring the mechanism of fluorescence quenching in proteins induced by tetracycline.

The binding of the antibiotic tetracycline hydrochloride (TC) to three proteins was investigated by steady-state, time-resolved, and circular dichroism spectroscopy. The tryptophan (Trp) amino acid residues were used as an intrinsic fluorophore to decipher the structure-function relationship. As monitored by CD spectroscopy, the addition of TC causes the protein to alter some of its helical content although such changes are only marginal. The gradual decrease in fluorescence intensity of Trp can be ascribed to static quenching which takes place by the interaction of the drug with the protein. Besides Trp quenching, there is evidence of fluorescence resonance energy transfer (FRET) in all three proteins with different values of efficiency of energy transfer. Various quenching/binding and thermodynamic parameters associated with such drug-protein interactions have been estimated. The results thus obtained can provide guidelines to synthetic chemists to design and synthesize target-oriented drugs.

Spectroscopic probing of the microenvironment in a protein-surfactant assembly.

The effect of the anionic surfactant sodium dodecyl sulfate (SDS) on the protein human serum albumin (HSA) was studied using steady-state spectroscopy, time-resolved measurements, and circular dichroism spectroscopy. The binding of SDS to the domain IIA of HSA, housing the single tryptophan amino acid residue (Trp214), was monitored, and it was found that this addition of the surfactant takes place in a sequential manner depending upon the concentration of the added surfactant. Both fluorescence intensity and lifetimes of HSA decreased with the increasing concentration of SDS, and the surfactant molecules serve the role of a quencher for the fluorescence of Trp214. Circular dichroism data also support the structural changes induced by SDS. The 17 disulfide bridges present in HSA provide the necessary structural rigidity to the protein. Stern-Volmer plots and thermodynamic parameters have been used to characterize the sequential binding of SDS to HSA, and these parameters not only confirm that the binding is spontaneous in nature but also is quite strong, depending on the concentration of the added surfactant.