Effect of sucrose on chemically and thermally induced unfolding of domain-I of human serum albumin: Solvation dynamics and fluorescence anisotropy study

An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch

The archetypical transcriptional crcB fluoride riboswitch from Bacillus cereus is an intricately structured non-coding RNA element enhancing gene expression in response to toxic levels of fluoride. Here, we used single molecule FRET to uncover three dynamically interconverting conformations appearing along the transcription process: two distinct undocked states and one pseudoknotted docked state. We find that the fluoride anion specifically snap-locks the magnesium-induced, dynamically docked state. The long-range, nesting, single base pair A40-U48 acts as the main linchpin, rather than the multiple base pairs comprising the pseudoknot. We observe that the proximally paused RNA polymerase further fine-tunes the free energy to promote riboswitch docking. Finally, we show that fluoride binding at short transcript lengths is an early step toward partitioning folding into the docked conformation. These results reveal how the anionic fluoride ion cooperates with the magnesium-associated RNA to govern regulation of downstream genes needed for fluoride detoxification of the cell.

Domain-Specific Stabilization of Structural and Dynamic Responses of Human Serum Albumin by Sucrose

Background:

Human Serum Albumin (HSA) is the most abundant protein present in human blood plasma. It is a large multi-domain protein with 585 amino acid residues. Due to its importance in human body, studies on the interaction of HSA with different external agent is of vital interest. The denaturation and renaturation of HSA in presence of external agents are of particular interest as they affect the biological activity of the protein.

Objective:

The objective of this work is to study the domain-specific and overall structural and dynamical changes occurring to HSA in the presence of a denaturing agent, urea and a renaturing agent, sucrose.

Methods:

In order to carry out the domain-specific studies, HSA has been tagged using N-(7- dimethylamino-4-methylcoumarin-3-yl) iodoacetamide (DACIA) at Cys-34 of domain-I and pnitrophenyl coumarin ester (NPCE) at Tyr-411 site in domain-III, separately. Steady-state absorption, emission and solvation dynamic measurements have been carried out in order to monitor the domain-specific alteration of HSA caused by the external agents. The overall structural change of HSA have been monitored using circular dichroism spectroscopy.

Results:

The α-helicity of HSA was found to decrease from 65% to 11% in presence of urea and was found to further increase to 25% when sucrose is added, manifesting the denaturing and renaturing effects of urea and sucrose, respectively. The steady state studies show that domain-III is more labile towards denaturation as compared to domain-I. The presence of an intermediate state is observed during the denaturation process. The stabilization of this intermediate state in presence of sucrose is attributed as the reason for the stabilization of HSA by sucrose. From solvation dynamics studies, it could be seen that the solvation time of DACIA inside domain-I of HSA decreases and increases regularly with increasing concentrations of urea and sucrose, respectively, while in the case of NPCE-tagged domain-III, the effect of sucrose on solvation time is evident only at high concentrations of urea.

Conclusion:

The denaturing and renaturing effects of urea and sucrose could be clearly seen from the steady state studies and circular dichroism spectroscopy measurements. A regular change in solvation time could only be observed in the case of domain-I and not in domain-III. The results indicate that the renaturing effect of sucrose on domain-III is not very evident when protein is in its native state, but is evident in when the protein is denatured.</P>

Region-Specific Double Denaturation of Human Serum Albumin: Combined Effects of Temperature and GnHCl on Structural and Dynamical Responses

In this work, we have investigated the effects of denaturing agents, guanidine hydrochloride (GnHCl) and temperature, on the overall structure, domain-I, and domain-III of human serum albumin (HSA) using circular dichroism (CD) spectroscopy and steady-state, time-resolved fluorescence spectroscopy. We have tagged Cys-34 of HSA, located at domain-I, using N-(7-dimethylamino-4-methylcoumarin-3-yl)iodoacetamide and Tyr-411 of HSA, located at domain-III, using p-nitrophenyl coumarin ester, for this purpose. The CD spectroscopy studies reveal the overall denaturation of the protein. The denaturation follows the expected direction in which the protein is denatured with an increase in the concentration of GnHCl or temperature. The α-helicity of the native state of HSA was found to be 64.2%, and the minimum value of α-helicity was found to be 14.8% in the presence of 6 M GnHCl at room temperature. Steady-state emission studies were carried out on domain-I and domain-III of the protein using site-specific fluorescent tags. The degree of folding of the two domains at different combinations of temperature and GnHCl concentration was calculated and was found to follow a slightly different course of denaturation. Solvation dynamics was found to be quite different for these two domains. The domain-I of HSA has a maximum solvation time of 0.39 ns, and the solvation time tends to decrease with the action of either temperature or GnHCl. On the other hand, the domain-III of HSA showed a much higher solvation time (1.42 ns) and does not show any regular change at higher temperatures or in the presence of GnHCl. This difference could be attributed to the different microenvironment inside the protein cores of the two domains.

Elucidation of active site dynamics of papain and the effect of encapsulation within cationic and anionic reverse micelles

In this study, steady state, solvation dynamics and rotational dynamics experiments have been carried out on a system of DACIA-tagged papain in bulk water and inside the water pool of cationic (cetyltrimethylammonium bromide, CTAB) and anionic (sodium bis(2-ethylhexyl)sulfosuccinate, AOT) reverse micelles with varying water contents (W₀ = 20 to 50). While the absorption and emission maxima and the excited state lifetime did not show any noticeable change with the variation of the size of the reverse micelle, the change in solvation time, Stokes shift, rotational correlation time and residual anisotropy with the change in reverse micellar size were quite revealing. The average solvation time and Stokes shift of papain in bulk water are 0.22 ns and 125 cm^-1 respectively, which increase to 0.96 ns and 718 cm^-1 while inside CTAB reverse micelle of W₀ = 20. The solvation time and Stokes shift values decrease with the increase in the size of reverse micelle, approaching the corresponding values in bulk water when W₀ = 50. The solvation time and Stokes shift of the DACIA-tagged papain was found to be high while inside AOT reverse micelle also (0.47 ns and 438 cm^-1 respectively when W₀ = 20), but there was no monotonous variation with the change in size of micellar size as in the case with CTAB reverse micelle. From the anisotropy studies, it was seen that inside CTAB and AOT reverse micelles, there is a significant amount of residual anisotropy, which is absent in the case of DACIA-tagged papain in bulk water. The rotational correlation times were also found to be higher inside the reverse micelles than those in bulk water. Both residual anisotropy and rotational correlation time were found to be more in the case with AOT reverse micelle than with CTAB reverse micelle. These behaviours could be explained based on the electrostatic forces acting between the papain having a positive surface charge and the reverse micelles of cationic CTAB and anionic AOT.

Elucidation of the local dynamics of domain-III of human serum albumin over the ps-μs time regime using a new fluorescent label

The ps-μs dynamics of domain-III of human serum albumin (HSA) has been investigated using a new fluorescent marker selectively labeled to the Tyr-411 residue. The location of the marker has been confirmed using Förster resonance energy transfer (FRET) study. Steady state, time-resolved and single molecular level fluorescence techniques have been employed to understand the dynamics within the domain-III of HSA. It is found that solvent reorganization dynamics in domain-III is 1.7 times faster than that in domain-I. The timescale of the local rotational dynamics of domain-III is found to be 2.3 times faster than that of domain-I. Fluorescence correlation spectroscopic experiments reveal that domain-III of HSA has more conformational flexibility than domain-I. Together, the results deliver useful details of the local environment around the domain-III of HSA, which have not been explored earlier, mainly because of a lack of a suitable fluorescent marker for domain-III. The newly synthesized probe serves well as a site specific fluorescent marker for HSA, and can be used for further investigation of the ligand binding properties and enzymatic activity of domain-III of HSA.

Site-directed fluorescence labeling of intrinsically disordered region of human transcription factor YY1: The inhibitory effect of zinc ions

Site-specific labeling of proteins with fluorescent dyes allows the study of protein structure and function using a wide variety of fluorescent techniques. However, specific labeling is not trivial in the case of proteins containing multiple cysteine residues. An example of such a protein is transcription factor Yin Yang 1, which comprises eight cysteine residues in four C2H2 type zinc fingers in the C-terminal region. Kinetic measurements of the labeling process allowed us to develop preparative labeling of three cysteine residues differently introduced to the N-terminal, disordered fragment of the protein. The protocol developed in the present study allows to prepare the protein with high recovery yield and high selectivity of the labeling. This was confirmed using proteolytic digestion and spectroscopic approach. The labeling process was significantly affected by the presence of zinc ions and was dependent on the localization of the engineered cysteine residue. This is the first known example of the use of cysteine metal protection and labeling (CyMPL) technology for the labeling of protein regions with no stable secondary structures.