Long-Range Modulations of Electric Fields in Proteins

Abstract

Electrostatic interactions are essential for controlling the protein structure and function. Whereas so far experimental and theoretical efforts focused on the effect of local electrostatics, this work aims at elucidating the long-range modulation of electric fields in proteins upon binding to charged surfaces. The study is based on cytochrome c (Cytc) variants carrying nitrile reporters for the vibrational Stark effect that are incorporated into the protein via genetic engineering and chemical modification. The Cytc variants were thoroughly characterized with respect to possible structural perturbations due to labeling. For the proteins in solution, the relative hydrogen bond occupancy and the calculated electric fields, both obtained from molecular dynamics (MD) simulations, and the experimental nitrile stretching frequencies were used to develop a relationship for separating hydrogen-bonding and non-hydrogen-bonding electric field effects. This relationship provides an excellent description for the stable Cytc variants in solution. For the proteins bound to Au electrodes coated with charged self-assembled monolayers (SAMs), the underlying MD simulations can only account for the electric field changes Δ E due to the formation of the electrostatic SAM-Cytc complexes but not for the additional contribution, Δ E, representing the consequences of the potential drops over the electrode/SAM/protein interfaces. Both Δ E and Δ E, determined at distances between 20 and 30 Å with respect to the SAM surface, are comparable in magnitude to the non-hydrogen-bonding electric field in the unbound protein. This long-range modulation of the internal electric field may be of functional relevance for proteins in complexes with partner proteins (Δ E) and attached to membranes (Δ E + Δ E).

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

“…To take into account the effect of an H-bond between OH group and nitrile N atom to the vibrational solvatochromism in an ad hoc manner, Biava et al modified the vibrational Stark effect theory considering two different CN groups, i.e., non-H-bonded and H-bonded nitriles. 336 They are then treated differently so that the net vibrational frequency shift of the CN stretch mode is expressed as a function of the fraction of the H-bonded species, HB The above results and failures in developing a rigorous and systematic theory for vibrational solvatochromism of CN stretching vibration in solutions suggest that the vibrational solvatochromic frequency shifts of the nitrile stretching mode result from various contributions from quadrupole and higher-order multipole terms and non-Coulomb interactions in addition to the dipolar term. By employing the Bio-SolEFP method for the vibrational frequency shift of the IR probe, Błasiak et al demonstrated that the nitrile stretching frequency shift due to Hbonding interaction with surrounding water molecules is determined not only by the contribution of Coulomb interactions but also by the dispersion interactions and the exchangerepulsion contributions.…”

A Critical Evaluation of Vibrational Stark Effect (VSE) Probes with the Local Vibrational Mode Theory

“…Given a simplified electrostatic description of non-covalent interactions between the vibrational probe and surrounding molecules, the strength of these intermolecular interactions can be assessed by the electric field a target chemical bond feels, as revealed by the VSE [5,13]. The VSE has been extensively applied to study the non-covalent interactions in different types of chemical systems and environments including proteins/enzymes [6][7][8]10,11,[14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33], nucleic acids [34,35], ionic liquids [36,37], biological membranes [38], electrochemical interfaces/surfaces [12,[39][40][41][42][43], and polymers [3,44,45]. Recently, the range of applications has been extended to the investigation of water clusters [46,47] and molecular solids [48].…”

Substrates modulate charge-reorganization allosteric effects in protein-protein association

“…This new concept of charge reorganization in proteins is consistent with the recent discovery of long range electron conduction in proteins 6 and the finding of long range modulation of electric field in proteins. 7…”