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1. Dynamic permittivity of confined water under a static background field

   https://doi.org/10.1063/5.0233894  

   Bratko, D; Mulpuri, N (October 2024, The Journal of Chemical Physics)

   Molecular and collective reorientations in interfacial water are by-and-large decelerated near surfaces subjected to outgoing electric fields (pointing from surface to liquid, i.e., when the surface carries positive charge). In incoming fields at negatively charged surfaces, these rates show a nonmonotonic dependence on field strength where fastest reorientations are observed when the field alignment barely offsets the polarizing effects due to interfacial hydrogen bonding. This extremum coincides with a peak of local static permittivity. We use molecular dynamics simulations to explore the impact of background static field on high frequency AC permittivity in hydration water under an electric field mimicking the conditions inside a capacitor where one of the confinement walls is subject to an outgoing field and the other one to an incoming field. At strong static fields, the absorption peak undergoes a monotonic blue shift upon increasing field strength in both hydration layers. At intermediate fields, however, the hydration region at the wall under an incoming field (the negative capacitor plate) features a red shift coinciding with maximal static-permittivity and reorientation-rate. The shift is mostly determined by the variation of the inverse static dielectric constant as proposed for mono-exponentially decaying polarization correlations. Conversely, hydration water at the opposite (positively charged) surface features a monotonic blue shift consistent with conventional saturation. The sensitivity of absorption peaks on the field suggests that surface charge densities could be deduced from sub-THz dielectric spectroscopy experiments in porous materials when interfaces accommodate a major fraction of water contained in the system. 

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2. Identifying hydrophobic protein patches to inform protein interaction interfaces

   https://doi.org/10.1073/pnas.2018234118  

   Rego, Nicholas B.; Xi, Erte; Patel, Amish J. (February 2021, Proceedings of the National Academy of Sciences)

   Interactions between proteins lie at the heart of numerous biological processes and are essential for the proper functioning of the cell. Although the importance of hydrophobic residues in driving protein interactions is universally accepted, a characterization of protein hydrophobicity, which informs its interactions, has remained elusive. The challenge lies in capturing the collective response of the protein hydration waters to the nanoscale chemical and topographical protein patterns, which determine protein hydrophobicity. To address this challenge, here, we employ specialized molecular simulations wherein water molecules are systematically displaced from the protein hydration shell; by identifying protein regions that relinquish their waters more readily than others, we are then able to uncover the most hydrophobic protein patches. Surprisingly, such patches contain a large fraction of polar/charged atoms and have chemical compositions that are similar to the more hydrophilic protein patches. Importantly, we also find a striking correspondence between the most hydrophobic protein patches and regions that mediate protein interactions. Our work thus establishes a computational framework for characterizing the emergent hydrophobicity of amphiphilic solutes, such as proteins, which display nanoscale heterogeneity, and for uncovering their interaction interfaces. 

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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. AC permittivity of confined water in the presence of static field

   https://doi.org/10.1021/scimeetings.5c10926  

   Bratko, D; Mulpuri, N (September 2024, ACS)

   Kinetics of molecular and collective reorientations at solid/water interfaces are known to depend on local electric field. Deceleration is observed near surfaces subjected to an outgoing static field (pointing from surface to liquid) as is the case when the solid carries positive charge. In an incoming field, both the reorientation rates and local permittivity in hydration layer show a nonmonotonic dependence on field strength with fastest reorientations and highest permittivity observed when the field alignment barely offsets the orienting bias at the wall. (Mulpuri and Bratko, J. Chem. Phys. 158,134716, 2023). Here, we use Molecular Dynamics simulations to explore the impact of background field (or, equivalently, surface charge density) on high frequency (GHz to THz) AC permittivity in hydration water inside a nanosized aqueous film under perpendicular DC field. Our model system mimics conditions inside a capacitor where one of the confinement walls is subject to outgoing and the other one to incoming field. In very strong static fields, the frequency corresponding to the maximal imaginary part of AC permittivity, features a blue shift with increasing field strength in both hydration layers. At intermediate fields, however, the hydration region at the wall under ingoing field (adjacent to the negative capacitor plate) features a red shift, which is especially pronounced at the field strength corresponding to the maxima of static-permittivity and reorientation-rate. The shift reflects the variation of the inverse static dielectric constant in normal direction, (Gekle and Netz, J. Chem. Phys. 137, 104704, 2012) with marginal effect of librational motions on the local AC permittivity. Hydration water at the opposite surface (closer to the positive capacitor plate), on the other hand, features a monotonic blue shift consistent with conventional saturation. The sensitivity of imaginary peaks on the field suggests surface charge densities could be deduced from THz dielectric spectroscopy experiments in a porous material where hydration layers comprise a major fraction of water contained in the system. 

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5. Hydrophobic Clusters Regulate Surface Hydration Dynamics of Bacillus subtilis Lipase A

   https://doi.org/10.1021/acs.jpcb.4c00405  

   Jaufer, Afnan M; Bouhadana, Adam; Fanucci, Gail E (April 2024, The Journal of Physical Chemistry B)

   na (Ed.)

   The surface hydration diffusivity of Bacillus subtilis Lipase A (BSLA) has been characterized by low-field Overhauser dynamic nuclear polarization (ODNP) relaxometry using a series of spin-labeled constructs. Sites for spin-label incorporation were previously designed via an atomistic computational approach that screened for surface exposure, reflective of the surface hydration comparable to other proteins studied by this method, as well as minimal impact on protein function, dynamics, and structure of BSLA by excluding any surface site that participated in greater than 30% occupancy of a hydrogen bonding network within BSLA. Experimental ODNP relaxometry coupling factor results verify the overall surface hydration behavior for these BSLA spin-labeled sites similar to other globular proteins. Here, by plotting the ODNP parameters of relative diffusive water versus the relative bound water, we introduce an effective "phase-space" analysis, which provides a facile visual comparison of the ODNP parameters of various biomolecular systems studied to date. We find notable differences when comparing BSLA to other systems, as well as when comparing different clusters on the surface of BSLA. Specifically, we find a grouping of sites that correspond to the spin-label surface location within the two main hydrophobic core clusters of the branched aliphatic amino acids isoleucine, leucine, and valine cores observed in the BSLA crystal structure. The results imply that hydrophobic clustering may dictate local surface hydration properties, perhaps through modulation of protein conformations and samplings of the unfolded states, providing insights into how the dynamics of the hydration shell is coupled to protein motion and fluctuations. 

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