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1. Investigating hydration dynamics and protein collective motions by high-precision dielectric spectroscopy

   https://doi.org/10.1117/12.2567857  

   Doan, Luan C; Nguyen, Vinh Q. (September 2020, Proceedings of SPIE)

   null (Ed.)

   Biological processes often take place at surfaces of proteins, where the dynamic and structural properties of aqueous solvents are modified. Information about solvent properties including hydration dynamics and structure, and protein collective motions can be obtained by measuring directly the dielectric response in the megahertz to terahertz frequencies of aqueous protein solutions. Due to the strong absorption of water in this frequency range, the experiment is challenging. Our home built dielectric spectrometer using a vector network analyzer together with frequency extenders allows us to perform the experiment in a wide range of frequency from megahertz to terahertz with a high dynamical range up to 120 dB. A detailed investigation of the dielectric response has revealed the hydration structure including the tightly, loosely bound layers and the number of water molecules in each hydration layer. These water molecules relax with different time constants at different temperatures. As a result, the dynamics of hydrated protein is also probed at different temperatures. Understanding the hydration structure and dynamics of lysozyme in biological conditions can explain the enzymatic activities of biomolecules. 

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2. Linear and Nonlinear Dielectric Response of Intrinsically Disordered Proteins

   https://doi.org/10.1021/acs.jpclett.4c00866  

   Sauer, Michael A; Colburn, Taylor; Maiti, Sthitadhi; Heyden, Matthias; Matyushov, Dmitry V (May 2024, The Journal of Physical Chemistry Letters)

   Scholes, Gregory D (Ed.)

   Linear and nonlinear dielectric responses of solutions of intrinsically disordered proteins (IDPs) were analyzed by combining molecular dynamics simulations with formal theories. A large increment of the linear dielectric function over that of the solvent is found and related to large dipole moments of IDPs. The nonlinear dielectric effect (NDE) of the IDP far exceeds that of the bulk electrolyte, offering a route to interrogate protein conformational and rotational statistics and dynamics. Conformational flexibility of the IDP makes the dipole moment statistics consistent with the gamma/log-normal distributions and contributes to the NDE through the dipole moment’s non-Gaussian parameter. The intrinsic non-Gaussian parameter of the dipole moment combines with the protein osmotic compressibility in the nonlinear dielectric susceptibility when dipolar correlations are screened by the electrolyte. The NDE is dominated by dipolar correlations when electrolyte screening is reduced. 

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3. Charge Distribution Patterns of IA ₃ Impact Conformational Expansion and Hydration Diffusivity of the Disordered Ensemble

   https://doi.org/10.1021/acs.jpcb.3c06170  

   Dunleavy, Katie M.; Li, Tianyan; Milshteyn, Eugene; Jaufer, Afnan M.; Walker, Shamon A.; Fanucci, Gail E. (November 2023, The Journal of Physical Chemistry B)

   Dr. Sudipta Maiti (Ed.)

   IA3 is a 68 amino acid natural peptide/protein inhibitor of yeast aspartic proteinase A (YPRA) that is intrinsically dis-ordered in solution with induced N-terminal helicity when in the protein complex with YPRA. Based upon the intrinsical-ly disordered proteins (IDPs) parameters of fractional net charge (FNC), of net charge density per residue (NCPR) and of charge patterning (), the two domains of IA3 are defined to occupy different domains within conformationally based subclasses of IDPs; thus, making IA3 a bimodal-domain IDP. Site-directed spin-labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy and low-field Overhauser dynamic nuclear polarization (ODNP) spectroscopy results show that these two domains possess different degrees of compaction and hydration diffusivity behavior. This work suggests that SDSL EPR line shapes – analyzed in terms of their local tumbling volume (VL) – provide insight into the compaction of the unstructured IDP ensemble in solution and that protein sequence and net charge distribution pat-terns within a conformational subclass can impact bound water hydration dynamics; thus, possibly offering an alter-native thermodynamic property that can encode conforma-tional binding and behavior of IDPs and liquid-liquid phase separations. 

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4. NMR approaches to identify transient structure and interactions of intrinsically disordered dynein intermediate chain

   https://doi.org/10.1016/j.jmb.2025.169380  

   Loening, Nikolaus M; Jara, Kayla A; Barbar, Elisar J (August 2025, Journal of Molecular Biology)

   Nuclear magnetic resonance (NMR) spectroscopy is widely recognized for its ability to provide atomic-level resolution of structures and interactions in intrinsically disordered proteins (IDPs). However, its application is often limited when studying large proteins that contain both structured and disordered regions. This challenge arises due to the broad peaks exhibited by structured regions in such proteins, which result from local compaction and restricted motions, complicating spectral analysis. Additionally, broadening in IDP complexes caused by exchange between free and bound states and/or the large size of the bound state, further obscures NMR signals and hinders the mapping of interaction sites. Moreover, IDPs are highly sensitive to proteolytic cleavage, necessitating careful handling and optimization during expression, purification, and data collection. In this study, we demonstrate how we successfully overcame these hurdles using examples from our work on the N-terminal region of the dynein intermediate chain (IC), which contains both ɑ-helical and intrinsically disordered regions. By employing paramagnetic relaxation enhancement (PRE) NMR to probe conformational dynamics, water-amide chemical exchange to measure solvent accessibility, and saturation transfer difference (STD) NMR to map specific interactions with p150^Glued and Nudel, we identified novel transient structures and interaction networks within IC. Our findings highlight the utility of these advanced NMR techniques in elucidating the dynamic behavior of IDPs and their complexes, providing valuable insights into their structural and functional roles. 

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5. Long-range DNA-water interactions

   https://doi.org/https://doi.org/10.1016/j.bpj.2021.10.016  

   Singh, Abhishek K; Wen, Chengyuan; Cheng, Shengfeng; Vinh, N. Q. (November 2021, Biophysical journal)

   DNA functions only in aqueous environments and adopts different conformations depending on the hydration level. The dynamics of hydration water and hydrated DNA leads to rotating and oscillating dipoles that, in turn, give rise to a strong megahertz to terahertz absorption. Investigating the impact of hydration on DNA dynamics and the spectral features of water molecules influenced by DNA, however, is extremely challenging because of the strong absorption of water in the megahertz to terahertz frequency range. In response, we have employed a high-precision megahertz to terahertz dielectric spectrometer, assisted by molecular dynamics simulations, to investigate the dynamics of water molecules within the hydration shells of DNA as well as the collective vibrational motions of hydrated DNA, which are vital to DNA conformation and functionality. Our results reveal that the dynamics of water molecules in a DNA solution is heterogeneous, exhibiting a hierarchy of four distinct relaxation times ranging from ~8 ps to 1 ns, and the hydration structure of a DNA chain can extend to as far as ~18 A from its surface. The low-frequency collective vibrational modes of hydrated DNA have been identified and found to be sensitive to environmental conditions including temperature and hydration level. The results reveal critical information on hydrated DNA dynamics and DNA-water interfaces, which impact the biochemical functions and reactivity of DNA. 

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